Attention: World-2DPAGE is no longer maintained. Previously submitted data can still be queried at World-2DPAGE
Repository.
A Make2D-DB II DATABASE: version 2.50, built 18-Jul-2006
Dumped on 2006-07-18
The Make2D-DB II Tool
- common
- database
- array_dim_length( text[], character varying[], integer[], double precision[], integer )
- get_month( integer )
- hex_to_int( character varying )
- int_to_hex( bigint )
- make2db_ascii_entry( character varying, integer, text )
- make2db_entryspot_mapping_methods_string( character varying, character varying, integer )
- make2db_format_entry( text, integer, text )
- make2db_last_release( )
- make2db_primary_accession( character varying )
- make2db_release_of_date( date, boolean, boolean )
- make2db_reunit_line( character varying, bpchar )
- make2db_rl_verify_type( integer, character varying )
- make2db_verify_mappingtechnique( character varying[] )
- substitute_text( text, character varying, character varying )
- core
- log
- public
Schema common
To do: generate and send automatically a unique - hidden - database identifier from ExPASy to the remote database,
then LOCK table.
Make also this identifier queriable from the remote main interface.
common.database Structure
| F-Key |
Name |
Type |
Description |
|
|
databaseidentifier |
character varying(32) |
NOT NULL
|
|
|
databasename |
character varying(128) |
NOT NULL
|
|
|
databasedescription |
text |
|
|
|
databaserelease |
integer |
NOT NULL
DEFAULT make2db_last_release()
|
|
|
databasesubrelease |
smallint |
|
|
|
databasereleasedate |
date |
NOT NULL
DEFAULT ('now'::text)::date
|
|
|
databasereleasenotes |
text |
|
|
|
databasemainsummary |
text |
|
|
|
databaseinterfaceuri |
text |
|
|
|
databaseinterfaceurinumber |
smallint |
DEFAULT 1
|
|
|
copyright |
text |
|
|
|
contact |
text |
|
Permissions which apply to common.database
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema common
Returns: smallint
Language: PLPGSQL
FUNCTION TO RETURN THE LENGTH OF THE N-DIMENSION OF AN ARRAY
Needed with postgreSQL prior to 7.4, otherwise use array_upper (array_lower)
Call function by 2 arguments, and use void {} for the others (there is a postgreSQL problem casting _TYPES[])
ex: array_dim_length(CAST('{}' AS TEXT[]), CAST(my_mappingTechniques AS VARCHAR[]), CAST('{}' AS INTEGER[]), CAST('{}' AS FLOAT[]), 1);
to evaluate the first dimension of an INT array!! (prior to potsgres 7.4)
-- FUNCTION TO RETURN THE LENGTH OF THE N-DIMENSION OF AN ARRAY
---------------------------------------------------------------
-- Needed with postgreSQL prior to 7.4, otherwise use array_upper (array_lower)
-- Call function by 2 arguments, and use void {} for the others (there is a postgreSQL problem casting _TYPES[])
-- ex: array_dim_length(CAST('{}' AS TEXT[]), CAST(my_mappingTechniques AS VARCHAR[]), CAST('{}' AS INTEGER[]), CAST('{}' AS FLOAT[]), 1);
-- to evaluate the first dimension of an INT array!! (prior to potsgres 7.4)
DECLARE
my_mappingTechniques_text ALIAS for $1;
my_mappingTechniques_varchar ALIAS for $2;
my_mappingTechniques_int ALIAS for $3;
my_mappingTechniques_float ALIAS for $4;
my_dimension ALIAS for $5;
my_ar_length INT2;
my_ar_length_string TEXT;
my_pos1 INT2;
my_pos2 INT2;
BEGIN
-- Since postgreSQL 7.4: use Numerical array_upper and array_lower rather then array_dims
IF array_dims(my_mappingTechniques_text) IS NOT NULL THEN my_ar_length_string := array_dims(my_mappingTechniques_text);
ELSE IF my_mappingTechniques_varchar IS NOT NULL THEN my_ar_length_string := array_dims(my_mappingTechniques_varchar);
ELSE IF my_mappingTechniques_int IS NOT NULL THEN my_ar_length_string := array_dims(my_mappingTechniques_int);
ELSE IF my_mappingTechniques_float IS NOT NULL THEN my_ar_length_string := array_dims(my_mappingTechniques_float);
ELSE RETURN NULL;
END IF; END IF; END IF; END IF;
IF my_ar_length_string IS NULL THEN RETURN NULL;
END IF;
IF my_dimension > 1 THEN
FOR ii IN 1..(my_dimension-1)
LOOP
my_pos1 := strpos(my_ar_length_string,']');
my_ar_length_string := substr(my_ar_length_string, my_pos1 + 1);
END LOOP;
END IF;
my_pos1 := strpos(my_ar_length_string,':');
my_pos2 := strpos(my_ar_length_string,']');
my_ar_length_string := substr(my_ar_length_string, my_pos1 +1, my_pos2 - my_pos1 -1);
IF my_ar_length_string !~ '^[0-9]+$' THEN RETURN NULL;
END IF;
my_ar_length := my_ar_length_string::INT2;
RETURN my_ar_length;
END;
Returns: bpchar
Language: PLPGSQL
FUNCTION TO CONVERT d MONTHS in MMM FORMAT
-- FUNCTION TO CONVERT d MONTHS in MMM FORMAT
----------------------------------------------
DECLARE
month_number ALIAS for $1;
month CHAR(3);
BEGIN
IF month_number = 1 THEN RETURN 'JAN'; ELSE IF month_number = 2 THEN RETURN 'FEB';
ELSE IF month_number = 3 THEN RETURN 'MAR'; ELSE IF month_number = 4 THEN RETURN 'APR';
ELSE IF month_number = 5 THEN RETURN 'MAY'; ELSE IF month_number = 6 THEN RETURN 'JUN';
ELSE IF month_number = 7 THEN RETURN 'JUL'; ELSE IF month_number = 8 THEN RETURN 'AUG';
ELSE IF month_number = 9 THEN RETURN 'SEP'; ELSE IF month_number = 10 THEN RETURN 'OCT';
ELSE IF month_number = 11 THEN RETURN 'NOV'; ELSE IF month_number = 12 THEN RETURN 'DEC';
ELSE RETURN 'XXX';
END IF; END IF; END IF; END IF; END IF; END IF; END IF; END IF; END IF; END IF; END IF; END IF;
END;
Returns: bigint
Language: PLPGSQL
FUNCTION TO CONVERT HEXADECIMAL TO INTEGER
-- FUNCTION TO CONVERT HEXADECIMAL TO INTEGER
---------------------------------------------
DECLARE
my_hex ALIAS for $1;
my_hex_str VARCHAR(64);
my_digit TEXT;
my_int INT8;
ii INT8;
BEGIN
my_hex_str = my_hex;
my_int := 0;
ii := 1;
WHILE length(my_hex_str) > 0
LOOP
my_digit := substr(my_hex_str, length(my_hex_str));
IF my_digit = 'A' THEN my_digit := '10';
ELSE IF my_digit = 'B' THEN my_digit := '11';
ELSE IF my_digit = 'C' THEN my_digit := '12';
ELSE IF my_digit = 'D' THEN my_digit := '13';
ELSE IF my_digit = 'E' THEN my_digit := '14';
ELSE IF my_digit = 'F' THEN my_digit := '15';
END IF; END IF; END IF; END IF; END IF; END IF;
my_hex_str := substr(my_hex_str, 1, length(my_hex_str) - 1);
my_int := my_int + (my_digit::INT4) * ii;
ii := ii * 16;
END LOOP;
RETURN my_int;
END;
Returns: character varying
Language: PLPGSQL
FUNCTION TO CONVERT INTEGER TO HEXADECIMAL
-- FUNCTION TO CONVERT INTEGER TO HEXADECIMAL
---------------------------------------------
DECLARE
my_int ALIAS for $1;
my_int_num INT8;
my_digit INT2;
my_car CHAR(1);
my_hex VARCHAR(64);
ii INT2;
BEGIN
my_int_num = my_int::TEXT;
my_hex := '';
ii := 16;
WHILE my_int_num > 0
LOOP
my_digit := mod(my_int_num, ii);
my_int_num := (my_int_num::FLOAT - my_digit::FLOAT) / ii;
IF my_digit = 10 THEN my_car := 'A';
ELSE IF my_digit = 11 THEN my_car := 'B';
ELSE IF my_digit = 12 THEN my_car := 'C';
ELSE IF my_digit = 13 THEN my_car := 'D';
ELSE IF my_digit = 14 THEN my_car := 'E';
ELSE IF my_digit = 15 THEN my_car := 'F';
ELSE my_car := my_digit::TEXT;
END IF; END IF; END IF; END IF; END IF; END IF;
my_hex := my_car::VARCHAR || my_hex;
END LOOP;
RETURN my_hex;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO FORMAT A VIEW (tmp) ENTRY FOR ASCII OUTPUT.
Call function by 3 arguments: (AC, line length, hide private annotations),
(output line length is formatted by make2db_format_entry(output, line length, hide private annotations))
-- FUNCTION TO FORMAT A VIEW (tmp) ENTRY FOR ASCII OUTPUT
---------------------------------------------------------
-- Call function by 3 arguments: (AC, line length, hide private annotations)
--(output line length is formatted by make2db_format_entry(output, line length, hide private annotations))
DECLARE
my_ac VARCHAR(32);
my_entry TEXT;
my_record RECORD;
my_line_length INT;
my_hide_private TEXT;
my_month TEXT;
my_month_converted TEXT;
my_ac_first RECORD;
BEGIN
SET DATESTYLE TO 'POSTGRES, EUROPEAN';
my_ac := $1;
IF my_ac = '' THEN
RETURN 'No entry was given. Please, try again.
';
END IF;
my_line_length := $2;
IF my_line_length <25 THEN
my_line_length = 75;
END IF;
my_hide_private := $3;
SELECT INTO my_ac_first common.make2db_primary_accession(my_ac) AS AC;
IF NOT FOUND THEN
RETURN 'There is currently no entry ' || my_ac || '. Please, try again.
';
ELSE
SELECT INTO my_record * FROM ViewEntry WHERE accession_number::VARCHAR(32) = my_ac_first.AC;
END IF;
my_entry := 'ID ' || my_record.identifier || ';';
IF (length(my_record.id_method) > 0) THEN
my_entry := my_entry || ' ' || my_record.id_method || '.';
END IF;
my_entry := my_entry || '
AC ' || my_record.accession_number || ';';
IF my_record.secondary_identifiers <> '--' AND my_record.secondary_identifiers <> '' THEN
my_entry := my_entry || ' ' || my_record.secondary_identifiers || ';';
END IF;
IF my_record.creation ~ ' [0-9]D' THEN -- escaped parenthesis with[0-9]) cause a BUG in postgres 7.4!!
my_record.creation := substr(my_record.creation, 1, 17) || '0' || substr(my_record.creation, 18);
END IF;
my_month := substr(my_record.creation, 4, 2);
my_month_converted := '-' || get_month(my_month::INT) || '-';
my_month := '-' || my_month || '-';
my_record.creation = substitute_text(my_record.creation, my_month, my_month_converted);
/*my_month = get_month(my_month::INT);
my_record.creation = substr(my_record.creation, 1, 3) || my_month || substr(my_record.creation, 6, length(my_record.creation) - 6) || ', Created)';*/
my_entry := my_entry || '
DT ' || my_record.creation || '.';
my_month := substr(my_record.version_2d, 4, 2);
my_month_converted := '-' || get_month(my_month::INT) || '-';
my_month := '-' || my_month || '-';
my_record.version_2d = substitute_text(my_record.version_2d, my_month, my_month_converted);
my_entry := my_entry || '
DT ' || my_record.version_2d || '.';
my_month := substr(my_record.version_general, 4, 2);
my_month_converted := '-' || get_month(my_month::INT) || '-';
my_month := '-' || my_month || '-';
my_record.version_general = substitute_text(my_record.version_general, my_month, my_month_converted);
my_entry := my_entry || '
DT ' || my_record.version_general || '.';
IF my_record.description <> '--' AND my_record.description <> '' THEN
my_entry := my_entry || '
DE ' || my_record.description || '.';
END IF;
IF my_record.genes <> '--' AND my_record.genes <> '' THEN
my_entry := my_entry || '
GN ' || substitute_text(my_record.genes, ' and ','
GN and
GN ') || ';';
END IF;
my_entry := my_entry || '
OS ' || my_record.organism || '.
OC ' || my_record.organism_classification || '.';
IF my_record.taxonomy_cross_reference <> '--' AND my_record.taxonomy_cross_reference <> '' THEN
my_entry := my_entry || '
OX ' || my_record.taxonomy_cross_reference || ';';
END IF;
IF my_record.masters <> '--' AND my_record.masters <> '' THEN
my_entry := my_entry || '
MT ' || my_record.masters || '.';
END IF;
my_entry := my_entry || '
IM ' || my_record.images || '.';
my_entry := my_entry || '
' || my_record.reference_lines;
IF my_record.free_comments <> '--' AND my_record.free_comments <> '' THEN
my_entry := my_entry || '
CC ' || substitute_text(my_record.free_comments,'
','
CC ');
END IF;
IF my_record.one_d_comments <> '--' AND my_record.one_d_comments <> '' THEN
my_entry := my_entry || '
1D ' || substitute_text(my_record.one_d_comments,'
','
1D ');
END IF;
IF my_record.one_d_blocks <> '--' AND my_record.one_d_blocks <> '' THEN
my_entry := my_entry || '
1D ' || substitute_text(my_record.one_d_blocks,'
','
1D ');
END IF;
IF my_record.two_d_comments <> '--' AND my_record.two_d_comments <> '' THEN
my_entry := my_entry || '
2D ' || substitute_text(my_record.two_d_comments,'
','
2D ');
END IF;
IF my_record.two_d_blocks <> '--' AND my_record.two_d_blocks <> '' THEN
my_entry := my_entry || '
2D ' || substitute_text(my_record.two_d_blocks,'
','
2D ');
END IF;
IF my_record.database_cross_reference <>'--' AND my_record.database_cross_reference <> '' THEN
my_record.database_cross_reference := substitute_text(my_record.database_cross_reference,'
','
DR ');
my_entry := my_entry || '
DR ' || my_record.database_cross_reference;
END IF;
my_entry := make2db_format_entry(my_entry, my_line_length, my_hide_private);
my_entry := my_entry || '//';
RETURN my_entry;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO GET A STRING OF ALL MAPPING METHODS FOR A SPECIFIC ENTRY SPOT
-- FUNCTION TO GET A STRING OF ALL MAPPING METHODS FOR A SPECIFIC ENTRY SPOT
----------------------------------------------------------------------------
DECLARE
my_ac VARCHAR(32);
my_spotID VARCHAR(16);
my_gelID INT;
my_record RECORD;
my_mapping_method_string TEXT;
BEGIN
my_ac := $1;
IF my_ac = '' THEN
RETURN '';
END IF;
my_spotID := $2;
IF my_spotID = '' THEN
RETURN '';
END IF;
my_gelID := $3;
IF my_gelID < 1 THEN
RETURN '';
END IF;
my_mapping_method_string := '';
FOR my_record IN -- grouped Mapping Methods, possibly over several lines
SELECT '{' || array_to_string(mappingtechnique,',') || '} ' AS mappingTechniqueString
FROM spotentrymappingtopic
WHERE ac = my_ac AND spotID = my_spotID AND gelID = my_gelID AND mappingTechnique IS NOT NULL ORDER BY 1
LOOP
my_mapping_method_string := my_mapping_method_string || my_record.mappingTechniqueString;
END LOOP;
IF (length(my_mapping_method_string) > 0) THEN
my_mapping_method_string := substr(my_mapping_method_string, 0, length(my_mapping_method_string));
END IF;
return my_mapping_method_string;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO FORMAT ENTRIES TO X CHARACTERS PER LINE.
Call function by 3 arguments: (full text, line length, hide private annotations)
-- FUNCTION TO FORMAT ENTRIES TO X CHARACTERS PER LINE
------------------------------------------------------
-- Call function by 3 arguments: (full text, line length, hide private annotations)
DECLARE
my_full_entry TEXT;
my_new_entry TEXT;
my_old_line TEXT;
my_old_line_copy TEXT;
my_assembled_part TEXT;
my_keyword VARCHAR(11);
my_line_length INT2;
my_spaces TEXT;
my_hide_private TEXT;
ii INT2;
jj INT2;
BEGIN
my_full_entry := $1;
my_line_length := $2;
my_hide_private := $3;
my_new_entry := '';
my_spaces := ' ';
IF substr(my_full_entry,length(my_full_entry)) <> '
' THEN
my_full_entry := my_full_entry || '
';
END IF;
IF my_line_length < 25 THEN
my_line_length = 75;
END IF;
-- substract the 5 caracters for the keyword and the spaces, add one to include the
my_line_length := my_line_length - 4;
ii := 0;
WHILE strpos(my_full_entry, '
') <> 0 AND ii < 999
LOOP
ii := ii +1;
my_old_line := substr(my_full_entry, 1, strpos(my_full_entry, '
'));
my_full_entry := substr(my_full_entry, strpos(my_full_entry, '
') +1);
my_old_line := substr(my_old_line, 1, length(my_old_line) - 1);
my_old_line_copy := my_old_line;
my_assembled_part := '';
IF (length(my_hide_private) > 0) AND (my_old_line_copy ~ my_hide_private)
THEN
my_old_line := ''; my_old_line_copy := '';
ELSE
IF substr(my_old_line, 3, 3) <> ' ' THEN
RETURN $1;
END IF;
-- remove any head spaces --
WHILE substr(my_old_line_copy,6,1) = ' '
LOOP my_old_line_copy = substr(my_old_line, 1, 5) || substr(my_old_line_copy, 7);
END LOOP;
my_keyword := substr(my_old_line, 1, 5);
my_old_line_copy := substr(my_old_line_copy, 6);
IF strpos(my_old_line_copy,' ') = 0 OR length(my_old_line_copy) <= my_line_length THEN
my_new_entry := trim(my_new_entry) || my_keyword || my_old_line_copy || '
';
ELSE
jj := 0;
WHILE strpos(my_old_line_copy, ' ') <> 0 AND jj < 999
LOOP
IF length(my_assembled_part) + (strpos(my_old_line_copy, ' ')) > my_line_length
AND my_assembled_part <> ''
THEN
my_new_entry := trim(my_new_entry || my_keyword || my_assembled_part) || '
';
my_spaces := ' ';
IF my_assembled_part ~* '^-!- [a-z]' THEN my_spaces = ' ';
END IF;
IF (my_keyword ~* '^[1-9]D' OR (my_keyword~* '^CC'))
AND length(my_keyword) = 5 THEN
IF my_keyword~* '^CC' THEN my_spaces := my_spaces || ' ';
END IF;
my_keyword := my_keyword || my_spaces;
END IF;
my_assembled_part := '';
ELSE
my_assembled_part := my_assembled_part ||
substr(my_old_line_copy, 1, strpos(my_old_line_copy, ' '));
my_old_line_copy := substr(my_old_line_copy, strpos(my_old_line_copy, ' ') + 1);
END IF;
END LOOP;
my_new_entry := trim(my_new_entry || my_keyword || my_assembled_part);
IF length(my_old_line_copy) > 0 THEN
my_new_entry := my_new_entry || ' ' || my_old_line_copy || '
';
END IF;
END IF;
END IF;
IF substr(my_new_entry, length(my_new_entry), 1) <> '
' THEN
my_new_entry := my_new_entry || '
';
END IF;
END LOOP;
RETURN my_new_entry;
END;
Returns: integer
Language: PLPGSQL
FUNCTION TO GET LAST GENERAL RELEASE NUMBER
-- FUNCTION TO GET LAST GENERAL RELEASE NUMBER
----------------------------------------------
BEGIN
RETURN max(Release.releaseNum) FROM Release;
END;
Returns: character varying
Language: PLPGSQL
FUNCTION TO GET THE PRIMARY ACCESSION NUMBER
-- FUNCTION TO GET THE PRIMARY ACCESSION NUMBER
-----------------------------------------------
DECLARE
ac_arg_init ALIAS for $1;
ac_arg VARCHAR(32);
my_record RECORD;
BEGIN
ac_arg = upper(ac_arg_init);
SELECT INTO my_record Entry.AC FROM Entry WHERE upper(Entry.AC) = ac_arg::NAME;
IF my_record.AC IS NOT NULL THEN RETURN ac_arg; END IF;
SELECT INTO my_record Entry.AC, Entry.ID FROM Entry WHERE upper(Entry.ID) = ac_arg::NAME;
IF my_record.AC IS NOT NULL THEN RETURN my_record.AC; END IF;
-- with SP entry spliting we may have several AC for the same econdary AC (return a list?)
SELECT INTO my_record SecondaryAC.AC FROM SecondaryAC WHERE upper(SecondaryAC.secondaryAC) = ac_arg::NAME LIMIT 1;
IF my_record.AC IS NOT NULL THEN RETURN my_record.AC; END IF;
RETURN NULL;
END;
Returns: real
Language: PLPGSQL
FUNCTION TO RETURN THE DATABASE RELEASE (SUB-RELEASE) FOR A GIVEN DATE
-- FUNCTION TO RETURN THE DATABASE RELEASE (and SUB-RELEASE) OF A GIVEN DATE
----------------------------------------------------------------------------
-- Call function by 3 arguments:
-- (DATE, TRUE for rather the next version or FALSE for rather the previous version, TRUE to include sub-release)
-- Returns Real format: version.subVersion (Where subVersion is [dd] - 0 filled - if subVersion >0 and <100)
DECLARE
my_date ALIAS for $1;
my_after ALIAS for $2;
my_return_data ALIAS for $3;
my_record RECORD;
my_pre_subRelease TEXT;
my_old_text TEXT;
my_new_text TEXT;
BEGIN
IF my_after IS FALSE THEN
SELECT INTO my_record releaseNum, subRelease FROM Release WHERE releaseDate <= my_date
ORDER BY (releaseNum *10000 + subRelease) DESC LIMIT 1;
ELSE
SELECT INTO my_record releaseNum, subRelease FROM Release WHERE releaseDate >= my_date
ORDER BY (releaseNum *10000 + subRelease) LIMIT 1;
END IF;
IF my_return_data IS FALSE THEN
RETURN my_record.releaseNum::REAL;
END IF;
IF NOT FOUND THEN
IF my_after IS FALSE THEN
SELECT INTO my_record min(releaseNum) as releaseNum, min(subRelease) as subRelease
FROM Release WHERE releaseNum = (SELECT min(releaseNum) FROM Release);
ELSE
SELECT INTO my_record max(releaseNum) as releaseNum, max(subRelease) as subRelease
FROM Release WHERE releaseNum = (SELECT max(releaseNum) FROM Release);
END IF;
END IF;
my_pre_subRelease := '';
IF (my_record.subRelease > 0 AND my_record.subRelease < 10) THEN
my_pre_subRelease := '0';
END IF;
RETURN (my_record.releaseNum || '.' || my_pre_subRelease || my_record.subRelease)::REAL;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO RETRIEVE AND CONCATENATE A LIST OF ENTRY FIELDS
-- FUNCTION TO RETRIEVE AND CONCATENATE A LIST OF ENTRY FIELDS
--------------------------------------------------------------
DECLARE
my_AC ALIAS for $1;
my_line ALIAS for $2;
my_reunited TEXT;
my_record RECORD;
my_record2 RECORD;
ii INT2;
my_temp1_txt TEXT;
my_temp2_txt TEXT;
my_temp2_txt_aa TEXT;
my_temp2_txt_pmf TEXT;
my_temp2_txt_msms TEXT;
my_temp2_txt_pepseq TEXT;
my_temp3_txt TEXT;
my_temp4_txt TEXT;
my_temp5_txt TEXT;
my_spot_nature TEXT;
my_maps_record RECORD;
my_last_master VARCHAR(32); -- used in 2D blocks
my_last_2d_method TEXT;
my_substituted_text TEXT;
BEGIN
IF my_line = 'AC' THEN
/************************/
FOR my_record IN
SELECT secondaryAC
FROM SecondaryAC
WHERE CAST(AC AS varchar(32)) = my_AC
ORDER BY 1
LOOP
IF my_reunited IS NULL
THEN
my_reunited := CAST(my_record.secondaryAC AS varchar(20));
ELSE
my_reunited := my_reunited || '; ' || CAST(my_record.secondaryAC AS varchar(50));
END IF;
--RAISE NOTICE 'stored: %', my_reunited;
END LOOP;
ELSE IF my_line = 'DE' THEN
/*****************************/
SELECT INTO my_record description FROM Entry WHERE CAST(Entry.AC AS varchar(32)) = my_AC;
my_reunited := my_record.description;
SELECT INTO my_record enzymeCode FROM EnzymeNomenclature WHERE CAST(EnzymeNomenclature.AC AS varchar(32)) = my_AC;
IF my_record.enzymeCode IS NOT NULL AND my_reunited !~ my_record.enzymeCode
THEN
my_reunited := my_reunited || ' (updated EC ' || my_record.enzymeCode || ')';
END IF;
ELSE IF my_line = 'IM' THEN
/*****************************/
FOR my_record IN
SELECT Gel.shortName
FROM Gel, EntryGelImage
WHERE CAST(EntryGelImage.AC AS varchar(32)) = my_AC AND EntryGelImage.gelID = Gel.gelID
AND Gel.showFlagSwitch IS TRUE AND EntryGelImage.showFlagSwitch IS TRUE
ORDER BY 1
LOOP
IF my_reunited IS NULL
THEN
my_reunited := CAST(my_record.shortName AS varchar(50));
ELSE
my_reunited := my_reunited || ', ' || CAST(my_record.shortName AS varchar(50));
END IF;
--RAISE NOTICE '%', my_record.shortName;
--RAISE NOTICE 'stored: %', my_reunited;
END LOOP;
ELSE IF my_line = 'MT' THEN
/*****************************/
FOR my_record IN
SELECT Gel.shortName
FROM Gel, EntryGelMasTer
WHERE CAST(EntryGelMasTer.AC AS varchar(32)) = my_AC AND EntryGelMasTer.gelID = Gel.gelID
AND Gel.showFlagSwitch IS TRUE AND EntryGelMaster.showFlagSwitch IS TRUE
ORDER BY 1
LOOP
IF my_reunited IS NULL
THEN
my_reunited := CAST(my_record.shortName AS varchar(50));
ELSE
my_reunited := my_reunited || ', ' || CAST(my_record.shortName AS varchar(50));
END IF;
END LOOP;
ELSE IF my_line = 'CC' THEN
/*****************************/
FOR my_record IN
SELECT CommentTopic.CommentTopicName, CommentEntryFreeText.commentFreeText
FROM CommentTopic, CommentEntryFreeText
WHERE CAST(CommentEntryFreeText.AC AS varchar(32)) = my_AC
AND CommentTopic.commentTopicID = CommentEntryFreeText.commentTopicID
ORDER BY 1,2
LOOP
IF my_reunited IS NULL
THEN
my_reunited := '-!- ' || CAST(my_record.commentTopicName AS varchar(64)) || ': ' || my_record.commentFreeText;
ELSE
my_reunited := my_reunited || '
-!- ' || CAST(my_record.commentTopicName AS varchar(64))
|| ': ' || my_record.commentFreeText;
END IF;
END LOOP;
ELSE IF my_line = '1C' OR my_line = '2C' THEN
/*************************************************/
IF my_line = '1C' THEN ii =1;
ELSE IF my_line = '2C' THEN ii =2;
END IF;
END IF;
FOR my_record IN
SELECT CommentTopic.commentTopicName, CommentEntry2D.commentFreeText
FROM CommentTopic, CommentEntry2D
WHERE CAST(CommentEntry2D.AC AS varchar(32)) = my_AC
AND CommentTopic.commentTopicID = CommentEntry2D.commentTopicID AND CommentEntry2D.gelDimension = ii
ORDER BY 1,2
LOOP
IF my_reunited IS NULL
THEN
my_reunited := '-!- ' || CAST(my_record.commentTopicName AS varchar(64)) || ': ' || my_record.commentFreeText;
ELSE
my_reunited := my_reunited || '
-!- ' || CAST(my_record.commentTopicName AS varchar(64))
|| ': ' || my_record.commentFreeText;
END IF;
END LOOP;
ELSE IF (my_line = '2D' OR my_line ='1D') THEN
/**************************************************/
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_make2db_reunit_2d_topics')
THEN
DELETE FROM buffer_make2db_reunit_2d_topics; -- No need to lock table (serializable level is set on)
ELSE
CREATE TEMPORARY TABLE buffer_make2db_reunit_2d_topics ( stockSpot VARCHAR(16), stockMe1 TEXT, stockMe2 TEXT, mapping BOOLEAN );
END IF;
my_reunited := '';
my_last_master := '';
FOR my_maps_record IN SELECT Gel.shortName, Gel.gelID FROM Gel, EntryGelImage
WHERE CAST(EntryGelImage.AC AS varchar(32)) = my_AC AND EntryGelImage.gelID = Gel.gelID
AND Gel.showFlagSwitch IS TRUE AND EntryGelImage.showFlagSwitch IS TRUE
ORDER BY 1
LOOP /* loop over each master */
my_temp1_txt := '';
my_temp2_txt := '';
my_temp2_txt_aa := '';
my_temp2_txt_pmf := '';
my_temp2_txt_msms := '';
my_temp2_txt_pepseq := '';
my_temp3_txt := '';
my_temp4_txt := '';
my_temp5_txt := '';
FOR my_record IN
-- -- MASS SPECTROMETRY data is not showed within the entry itself
SELECT Gel.shortName, ViewSpotEntry.spotID, ViewSpotEntry.gelID, ViewSpotEntry.AC,
ViewSpotEntry.fragment, ViewSpotEntry.AminoAcidList, ViewSpotEntry.aa_version,
ViewSpotEntry.peptideSequences, ViewSpotEntry.peptseq_version,
ViewSpotEntry.peptideMasses, ViewSpotEntry.pmf_version,
ViewSpotEntry.msms, ViewSpotEntry.ms_version,
Spot.mw, Spot.pI
FROM Gel, ViewSpotEntry, Spot
WHERE Gel.shortName = my_maps_record.shortName
AND Gel.gelID = Spot.gelID
AND CAST(ViewSpotEntry.AC AS varchar(32)) = my_AC
AND ViewSpotEntry.spotID = Spot.spotID
AND ViewSpotEntry.gelID = Spot.gelID
ORDER BY ViewSpotEntry.spotID
LOOP /* lines of current master */
IF (my_record.shortName = ''
OR (my_line = '1D' AND my_record.pI IS NOT NULL)
OR (my_line = '2D' AND my_record.pI IS NULL))
THEN EXIT;
END IF;
IF my_last_master <> my_maps_record.shortName THEN
my_reunited := my_reunited || my_temp2_txt;
my_temp1_txt := '';
my_temp2_txt := '';
my_temp2_txt_aa := '';
my_temp2_txt_pmf := '';
my_temp2_txt_msms := '';
my_temp2_txt_pepseq := '';
my_temp3_txt := '';
my_reunited := my_reunited || '
-!- MASTER: ' || my_record.shortName || ';';
my_last_master := my_record.shortName;
END IF;
IF my_line = '2D' THEN
IF trunc(my_record.pI) < 10 THEN my_temp1_txt := substr(to_char(my_record.pI, '0d00'),2);
ELSE my_temp1_txt := substr(to_char(my_record.pI, '00d00'),2);
END IF;
my_spot_nature := 'SPOT';
my_reunited := my_reunited || '
-!- PI/MW: SPOT ' || my_record.spotID || '=';
my_reunited := my_reunited || my_temp1_txt || '/';
my_reunited := my_reunited || CAST(my_record.mw AS varchar(8)) || ';';
ELSE
my_spot_nature := 'BAND';
my_reunited := my_reunited || '
-!- MW: BAND ' || my_record.spotID || '=';
my_reunited := my_reunited || CAST(my_record.mw AS varchar(8)) || ';';
END IF;
IF my_record.fragment = 'true' THEN my_reunited := my_reunited || ' !FRAGMENT!';
END IF;
/* Identification Methods */
-- a line-feed is the separator for several data sets
-- MASS SPECTROMETRY data is not showed within the entry itself
IF my_record.AminoAcidList IS NOT NULL THEN
my_record.AminoAcidList := '
' || my_record.AminoAcidList;
my_substituted_text = ';
-!- AMINO ACID COMPOSITION: ' || my_spot_nature || ' ' || my_record.spotID || ': ';
my_record.AminoAcidList := common.substitute_text(my_record.AminoAcidList,'
', my_substituted_text);
my_temp2_txt_aa := my_temp2_txt_aa || substr(my_record.AminoAcidList,2) || ';';
END IF;
IF my_record.peptideMasses IS NOT NULL THEN
IF (strpos(my_record.peptideMasses,' [Documents] ') >0) THEN
-- when [Documents] was at the end of the field:
-- my_record.peptideMasses := substr(my_record.peptideMasses, 1, (strpos(my_record.peptideMasses,' [Documents] ')-1));
-- now, it is on its beginning, on a separate line:
my_record.peptideMasses := substr(my_record.peptideMasses, (strpos(my_record.peptideMasses,'
')+1));
IF (length(my_record.peptideMasses) < 1) THEN -- only documents
my_record.peptideMasses := '0';
END IF;
END IF;
my_record.peptideMasses := '
' || my_record.peptideMasses;
my_substituted_text = '.
-!- PEPTIDE MASSES: ' || my_spot_nature || ' ' || my_record.spotID || ': ';
my_record.peptideMasses := common.substitute_text(my_record.peptideMasses,'
', my_substituted_text);
my_temp2_txt_pmf := my_temp2_txt_pmf || substr(my_record.peptideMasses,2) || '.';
END IF;
IF my_record.msms IS NOT NULL THEN
IF (strpos(my_record.msms,' [Documents] ') >0) THEN
-- my_record.msms := substr(my_record.msms, 1, (strpos(my_record.msms,' [Documents] ')-1));
my_record.msms := substr(my_record.msms, (strpos(my_record.msms,'
')+1));
IF (length(my_record.msms) < 1) THEN -- only documents
my_record.msms := '[0:0]';
END IF;
END IF;
my_record.msms := '
' || my_record.msms;
my_substituted_text = '
-!- TANDEM MASS SPECTROMETRY: ' || my_spot_nature || ' ' || my_record.spotID || ': ';
my_record.msms := common.substitute_text(my_record.msms,'
', my_substituted_text);
my_temp2_txt_msms := my_temp2_txt_msms || substr(my_record.msms,1);
END IF;
IF my_record.peptideSequences IS NOT NULL THEN
my_record.peptideSequences := '
' || my_record.peptideSequences;
my_substituted_text = '.
-!- PEPTIDE SEQUENCES: ' || my_spot_nature || ' ' || my_record.spotID || ': ';
my_record.peptideSequences := common.substitute_text(my_record.peptideSequences,'
', my_substituted_text);
my_temp2_txt_pepseq := my_temp2_txt_pepseq || substr(my_record.peptideSequences,2) || '.';
END IF;
/* stock topics of current spot */
IF EXISTS ( SELECT * FROM SpotEntryGeneralTopic WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND CAST(AC AS VARCHAR(32)) = my_AC LIMIT 1)
THEN
INSERT INTO buffer_make2db_reunit_2d_topics (stockSpot, stockMe1, stockMe2, mapping)
SELECT my_record.spotID::VARCHAR(16), GeneralTopicDefinition.topicName::TEXT, GeneralTopicEntryData.topicDataText::TEXT, FALSE
FROM SpotEntryGeneralTopic, GeneralTopicEntryData, GeneralTopicDefinition
WHERE SpotEntryGeneralTopic.spotID = my_record.spotID
AND SpotEntryGeneralTopic.gelID = my_record.gelID
AND CAST(SpotEntryGeneralTopic.AC AS VARCHAR(32)) = my_AC
AND GeneralTopicEntryData.topicDataID = SpotEntryGeneralTopic.topicDataID
AND GeneralTopicEntryData.generalTopicID = GeneralTopicDefinition.generalTopicID
ORDER BY GeneralTopicDefinition.topicName, GeneralTopicEntryData.topicDataText;
-- we will not use regular expressions over my_temp4.txt as the fields may contain special characters (no function to escape them in PL/pgsql)
END IF;
/* stock mapping methods of current spot */
IF EXISTS ( SELECT * FROM SpotEntryMappingTopic WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND CAST(AC AS VARCHAR(32)) = my_AC LIMIT 1)
THEN
INSERT INTO buffer_make2db_reunit_2d_topics (stockSpot, stockMe1, stockMe2, mapping)
SELECT my_record.spotID::VARCHAR(16), GeneralTopicDefinition.topicName::TEXT, GeneralTopicEntryData.topicDataText::TEXT, TRUE
FROM SpotEntryMappingTopic, GeneralTopicEntryData, GeneralTopicDefinition
WHERE SpotEntryMappingTopic.spotID = my_record.spotID
AND SpotEntryMappingTopic.gelID = my_record.gelID
AND CAST(SpotEntryMappingTopic.AC AS VARCHAR(32)) = my_AC
AND GeneralTopicEntryData.topicDataID = SpotEntryMappingTopic.topicDataID
AND GeneralTopicEntryData.generalTopicID = GeneralTopicDefinition.generalTopicID
ORDER BY GeneralTopicDefinition.topicName, GeneralTopicEntryData.topicDataText;
-- we will not use regular expressions over my_temp5.txt as the fields may contain special characters (no
END IF;
END LOOP; /* end loop over lines of current master */
my_temp2_txt := my_temp2_txt_aa || my_temp2_txt_pmf || my_temp2_txt_msms || my_temp2_txt_pepseq;
/* write topics of current spot */
my_last_2d_method := '';
FOR my_record2 IN
SELECT DISTINCT stockMe1, stockMe2 FROM buffer_make2db_reunit_2d_topics WHERE mapping IS FALSE
ORDER BY stockMe1, stockMe2
LOOP
IF (my_record2.stockMe1 = my_last_2d_method) THEN
my_temp4_txt := substr(my_temp4_txt, 0, length(my_temp4_txt));
my_temp4_txt := my_temp4_txt || '; ' || my_record2.stockMe2 || '.';
ELSE
my_temp4_txt := my_temp4_txt || '
-!- ' || my_record2.stockMe1 || ': ' || my_record2.stockMe2 || '.';
END IF;
my_last_2d_method := my_record2.stockMe1;
END LOOP;
/* write mapping methods of current spot */
my_last_2d_method := '';
FOR my_record2 IN
SELECT DISTINCT stockMe1, stockMe2 FROM buffer_make2db_reunit_2d_topics WHERE mapping IS TRUE
ORDER BY stockMe1, stockMe2
LOOP
IF (my_record2.stockMe1 = my_last_2d_method) THEN
my_temp5_txt := substr(my_temp5_txt, 0, length(my_temp5_txt));
my_temp5_txt := my_temp5_txt || '; ' || my_record2.stockMe2 || '.';
ELSE
my_temp5_txt := my_temp5_txt || '
-!- ' || my_record2.stockMe1 || ': ' || my_record2.stockMe2 || '.';
END IF;
my_last_2d_method := my_record2.stockMe1;
END LOOP;
DELETE FROM buffer_make2db_reunit_2d_topics;
my_reunited := my_reunited || my_temp2_txt || my_temp3_txt || my_temp4_txt || my_temp5_txt;
END LOOP; /* end loop over each master */
-- DROP TABLE buffer_make2db_reunit_2d_topics;
my_reunited := substr(my_reunited, 2, length(my_reunited)); -- cut off first
ELSE IF my_line = 'DR' THEN
/*****************************/
FOR my_record IN
SELECT XrefDB.XrefDBName, EntryXrefDB.XrefPrimaryIdentifier, EntryXrefDB.XrefSecondaryIdentifier,
EntryXrefDB.XrefTertiaryIdentifier, EntryXrefDB.XrefOtherIdentifiers
FROM XrefDB, EntryXrefDB
WHERE CAST(EntryXrefDB.AC AS varchar(32)) = my_AC
AND EntryXrefDB.XrefDBCode = XrefDB.XrefDBCode AND activated IS TRUE
UNION
(SELECT XrefDBDynamic.XrefDBName, EntryXrefDBDynamic.XrefPrimaryIdentifier, EntryXrefDBDynamic.XrefSecondaryIdentifier,
EntryXrefDBDynamic.XrefTertiaryIdentifier, EntryXrefDBDynamic.XrefOtherIdentifiers
FROM XrefDBDynamic, EntryXrefDBDynamic
WHERE CAST(EntryXrefDBDynamic.AC AS varchar(32)) = my_AC
AND EntryXrefDBDynamic.XrefDBCode = XrefDBDynamic.XrefDBCode AND activated = 'true'
ORDER BY 1)
ORDER BY 1
LOOP
IF my_reunited IS NULL
THEN
my_reunited := my_record.XrefDBName || '; ' || CAST (my_record.XrefPrimaryIdentifier AS varchar(32));
ELSE
my_reunited := my_reunited || '
' || my_record.XrefDBName || '; '
|| CAST (my_record.XrefPrimaryIdentifier AS varchar(32));
END IF;
IF my_record.XrefSecondaryIdentifier IS NOT NULL
THEN
my_reunited := my_reunited || '; ' || CAST (my_record.XrefSecondaryIdentifier AS varchar(64));
END IF;
IF my_record.XrefTertiaryIdentifier IS NOT NULL
THEN
my_reunited := my_reunited || '; ' || CAST (my_record.XrefTertiaryIdentifier AS varchar(64));
END IF;
IF my_record.XrefOtherIdentifiers IS NOT NULL
THEN
my_reunited := my_reunited || '; ' || CAST (my_record.XrefOtherIdentifiers AS varchar(64));
END IF;
my_reunited := my_reunited || '.';
END LOOP;
-- This is the last line for a given entry
RAISE NOTICE '...entry % is processed', my_AC;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
IF my_reunited IS NULL OR my_reunited = '' THEN my_reunited := '--';
END IF;
RETURN my_reunited;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO CHECK THAT referenceLocationID ARE DIFFERENT FROM referenceType IN ReferenceLocation TABLES
-- FUNCTION TO CHECK THAT referenceLocationID ARE DIFFERENT FROM referenceType IN ReferenceLocation TABLES
----------------------------------------------------------------------------------------------------------
DECLARE
rl_id ALIAS for $1;
table_type ALIAS for $2;
my_type VARCHAR(32); -- ReferenceType.referenceType%TYPE; (produces a bug with postgreSQL 8.0 beta4!, even preceeded by core.)
BEGIN
SELECT INTO my_type ReferenceType.referenceType FROM ReferenceType, Reference
WHERE Reference.referenceID = rl_id AND Reference.referenceTypeID = ReferenceType.referenceTypeID
AND ReferenceType.referenceType = table_type;
IF NOT FOUND THEN
IF table_type = 'OTHER' THEN
-- any other defined category with no associated table and found in "OTHER" is also OK!
SELECT INTO my_type ReferenceType.referenceType FROM ReferenceType, Reference
WHERE Reference.referenceID = rl_id;
IF FOUND THEN RETURN 'true';
END IF;
END IF;
RETURN 'false';
END IF;
RETURN 'true';
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO VERIFY THAT METHODS IN THE ARRAY OF MAPPING METHODS ARE LISTED IN MappingTopicDefinition
Used as a CHECK constraint in SpotEntryMappingTopic
-- FUNCTION TO VERIFY THAT METHODS IN THE ARRAY OF MAPPING METHODS ARE LISTED IN MappingTopicDefinition
-------------------------------------------------------------------------------------------------------
-- Used as a CHECK constraint in SpotEntryMappingTopic
DECLARE
my_mappingTechniques ALIAS for $1;
my_ar_length INT2;
BEGIN
-- extract the length of the first dimension
my_ar_length :=
common.array_dim_length(CAST('{}' AS TEXT[]), CAST(my_mappingTechniques AS VARCHAR[]), CAST('{}' AS INTEGER[]), CAST('{}' AS FLOAT[]), 1);
IF (my_ar_length IS NULL OR my_ar_length < 1) THEN RETURN 'false';
END IF;
FOR ii IN 1..(my_ar_length)
LOOP
IF NOT EXISTS (SELECT * FROM MappingTopicDefinition WHERE mappingTechnique = my_mappingTechniques[ii])
THEN
RETURN 'false';
END IF;
END LOOP;
RETURN 'true';
END;
Returns: text
Language: PLPGSQL
FUNCTION TO SUBSTITUTE A PATTERN BY ANOTHER ONE IN A TEXT
-- FUNCTION TO SUBSTITUTE A PATTERN BY ANOTHER ONE IN A TEXT
------------------------------------------------------------
DECLARE
my_pattern_1 ALIAS for $2;
my_pattern_2 ALIAS for $3;
my_old_text TEXT;
my_new_text TEXT;
BEGIN
my_old_text := $1;
IF strpos(my_old_text, my_pattern_1) = 0 THEN
RETURN my_old_text;
END IF;
my_new_text := '';
WHILE strpos(my_old_text, my_pattern_1) <> 0
LOOP
my_new_text := my_new_text || substr(my_old_text, 1, strpos(my_old_text, my_pattern_1) -1)
|| my_pattern_2;
my_old_text := substr(my_old_text, strpos(my_old_text, my_pattern_1) + length(my_pattern_1),
length(my_old_text));
END LOOP;
RETURN my_new_text || my_old_text;
END;
Schema core
To apply any changes performed on the main core tables on the views (View* tables) and the public schema, execute the core.make2db_update(int,int) function with: SELECT core.make2db_update(1,1) -- see comments on this function for arguments description.
core.analyte Structure
| F-Key |
Name |
Type |
Description |
|
|
analyteid |
serial |
PRIMARY KEY
|
|
core.sample.sampleid
|
sampleid |
integer |
A trigger inserts sampleID from parent if child has parent (analyteParentID),
Should be "Not NULL", but is not for more flexibility
* Applied Trigger: Trigger_Analyte_sampleIDTracker *
|
|
core.analytepreparation.analytepreparationid
|
analytepreparationid |
integer |
|
|
|
description |
text |
|
|
core.analyte.analyteid
|
analyteparentid |
integer |
|
|
core.analyzable.analyzableid
|
fromanalyzablesource |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.analyte Constraints
| Name |
Constraint |
| analyte_check |
CHECK ((((fromanalyzablesource IS NULL) AND (analyteparentid IS NULL)) OR ((fromanalyzablesource IS NOT NULL) AND (analyteparentid IS NOT NULL)))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.analyte
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.analytepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
analytepreparationid |
serial |
PRIMARY KEY
|
|
|
preparationprotocol |
text |
|
|
|
uri |
character varying(4096) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.analytepreparation
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
In the future: with Analyte children referencing an "Analyzable" class (super-class?)
that containis all various "subAnalyzable" (e.g. Gel, LC,..) from which the children are obtained.
Otherwise, use just a simple relational correspondance.
core.analyzable Structure
| F-Key |
Name |
Type |
Description |
|
|
analyzableid |
serial |
PRIMARY KEY
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.analyzable
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.author Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
UNIQUE#1
NOT NULL
|
|
core.reference.referenceid
|
article |
integer |
UNIQUE#1
NOT NULL
|
|
|
authorpriority |
smallint |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.author
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.authorgroup Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
UNIQUE#1
NOT NULL
|
|
core.reference.referenceid
|
article |
integer |
UNIQUE#1
NOT NULL
Article reference could be limited only to e.g. ReferenceLocationSubmission and ReferenceLocationJournal
|
|
|
authorpriority |
smallint |
NOT NULL
DEFAULT 1
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.authorgroup
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.authorparent Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
NOT NULL
|
|
core.reference.referenceid
|
article |
integer |
NOT NULL
|
|
|
authorpriority |
smallint |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.authorparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.biologicalprocess Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goid |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.biologicalprocess Constraints
| Name |
Constraint |
| geneontologyparent_mappedenzymeclassification_check |
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)) |
Permissions which apply to core.biologicalprocess
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.biosource
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Biological source can be defined at various levels (for more flexibility).
core.biosourceinformation Structure
| F-Key |
Name |
Type |
Description |
|
|
biosourceinformationid |
serial |
PRIMARY KEY
|
|
core.organism.organismid
|
organismid |
integer |
NOT NULL
|
|
|
organismstrain |
character varying(256) |
|
|
|
straindetailsdescription |
text |
|
|
|
individualscount |
character varying(256) |
|
|
|
genotype |
character varying(16) |
|
|
|
developmentalstage |
character varying(256) |
|
|
|
anatomy |
character varying(256) |
|
|
core.tissue.tissueid
|
tissueid |
integer |
|
|
|
cell |
character varying(256) |
|
|
|
cellline |
character varying(256) |
|
|
|
measuredproperties |
text |
|
|
|
environmet |
character varying(256) |
|
|
|
treatment |
text |
|
|
|
phenotype |
text |
|
|
|
behaviour |
text |
|
|
|
pathology |
text |
|
|
|
provider |
character varying(256) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.biosourceinformation
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.biosourcepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
biosourcepreparationid |
serial |
PRIMARY KEY
|
|
|
preparationprotocol |
text |
|
|
|
uri |
character varying(4096) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.biosourcepreparation
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.book Structure
| F-Key |
Name |
Type |
Description |
|
|
bookid |
serial |
PRIMARY KEY
|
|
|
booktitle |
character varying(256) |
UNIQUE
NOT NULL
|
|
|
editors |
character varying(256) |
NOT NULL
|
|
|
publisher |
character varying(128) |
NOT NULL
|
|
|
city |
character varying(64) |
NOT NULL
|
|
|
year |
smallint |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.book Constraints
| Name |
Constraint |
| book_year_check |
CHECK (("year" > 0)) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.book
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.cellularcomponent Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goid |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.cellularcomponent Constraints
| Name |
Constraint |
| geneontologyparent_mappedenzymeclassification_check |
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)) |
Permissions which apply to core.cellularcomponent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
FOREIGN KEY (article, unpublished) REFERENCES ReferenceLocationJournal(referenceID, unpublished)
-> but not defined as UNIQUE in ReferenceLocationJournal
core.citer Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
UNIQUE#1
NOT NULL
|
|
core.referencelocationjournal.referenceid
|
article |
integer |
UNIQUE#1
NOT NULL
|
|
|
authorpriority |
smallint |
NOT NULL
|
|
|
unpublished |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.citer Constraints
| Name |
Constraint |
| citer_unpublished_check |
CHECK ((unpublished = true)) |
Permissions which apply to core.citer
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.commententry2d Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
|
|
core.commenttopic.commenttopicid
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
NOT NULL
|
|
|
geldimension |
smallint |
DEFAULT 2
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.commententry2d Constraints
| Name |
Constraint |
| commententry2d_geldimension_check |
CHECK (((geldimension = 1) OR (geldimension = 2))) |
Permissions which apply to core.commententry2d
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.commententryfreetext Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
|
|
core.commenttopic.commenttopicid
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.commententryfreetext
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.commententryparent Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
|
|
core.commenttopic.commenttopicid
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.commententryparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.commenttopic Structure
| F-Key |
Name |
Type |
Description |
|
|
commenttopicid |
serial |
PRIMARY KEY
|
|
|
commenttopicname |
character varying(64) |
UNIQUE
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.commenttopic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Contact person/institution is different and distinct than references.
Currently applied (optional) on projects, samples, gel preparations, gel informatics and spot analysis
core.contact Structure
| F-Key |
Name |
Type |
Description |
|
|
contactid |
serial |
PRIMARY KEY
|
|
|
name |
character varying(256) |
NOT NULL
|
|
|
email |
character varying(256) |
|
|
|
institution |
character varying(256) |
|
|
|
address |
text |
|
|
|
remark |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.contact
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
ID (0) is the default local interface.
To do: extend to all available interfaces via ExPASy
core.dynamicremotemake2ddbinterface Structure
| F-Key |
Name |
Type |
Description |
|
|
interfaceid |
serial |
PRIMARY KEY
|
|
|
interfaceuri |
text |
UNIQUE#1
NOT NULL
|
|
|
dbnumber |
integer |
UNIQUE#1
DEFAULT 1
|
|
|
dbname |
character varying(128) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.dynamicremotemake2ddbinterface
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
The term "Entry" has been prefered more than the term "Protein".
The Entry entity defines an alternative perspective (the widely used protein based view) to represent data.
* Applied Trigger: Trigger_Entry_AC_upperCase *
* Applied Trigger, DEPRECATED!: Trigger_Entry_synchronizeGeneralAndMapAnnotationFlags *
* Applied Trigger: Trigger_Entry_annotationChanged *
* Applied Trigger: Trigger_Entry_showFlagSwitchTrue *
core.entry Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
PRIMARY KEY
|
|
|
id |
character varying(32) |
UNIQUE
NOT NULL
|
|
|
entryclass |
character varying(32) |
DEFAULT 'STANDARD'::character varying
|
|
|
identmethod |
character varying(16) |
DEFAULT '2DG'::character varying
|
|
|
description |
text |
|
|
core.release.releasenum#1
|
releasecreation |
integer |
NOT NULL
DEFAULT 1
|
|
core.release.subrelease#1
|
subreleasecreation |
integer |
NOT NULL
|
|
|
genenames |
character varying(1024) |
|
|
|
keywords |
character varying(1024) |
|
|
core.organism.organismid
|
organismid |
integer |
At the protein level, the annotated organism is not forcibly the same as for the analyzed sample
|
|
|
organismstrain |
character varying(256) |
|
|
|
entrychecksum |
character(16) |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.entry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Corresponds to the SWISS-2DPAGE "IM" (IMage) line.
* Applied Trigger: Trigger_EntryGelImage_showFlagSwitchTrue *
core.entrygelimage Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
PRIMARY KEY
|
|
core.gel.gelid
|
gelid |
integer |
PRIMARY KEY
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entrygelimage
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Corresponds to the SWISS-2DPAGE "MT" (MasTer) line [Specific to SWISS-2DPAGE].
* Applied Trigger: Trigger_EntryGelMaster_showFlagSwitchTrue *
core.entrygelmaster Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
PRIMARY KEY
|
|
core.gel.gelid
|
gelid |
integer |
PRIMARY KEY
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entrygelmaster
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
This table content is not used *for the moment* by the entry views! (to do: Entry.geneNames dynamically constructed from this table)
core.entrygene Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
core.genename.geneid
|
geneid |
integer |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entrygene
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.entrytheoreticalpimw Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
NOT NULL
|
|
|
modifiedproteindescription |
text |
|
|
|
theoreticalpi |
numeric(4,2) |
NOT NULL
|
|
|
theoreticalmw |
integer |
NOT NULL
|
|
|
algorithmoriginandversion |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entrytheoreticalpimw
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.entryversion2d Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
PRIMARY KEY
|
|
|
version |
integer |
NOT NULL
DEFAULT 1
|
|
|
versiondate |
date |
NOT NULL
DEFAULT ('now'::text)::date
|
|
|
annotationchanged |
boolean |
DEFAULT false
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryversion2d
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.entryversiongeneral Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
PRIMARY KEY
|
|
|
version |
integer |
NOT NULL
DEFAULT 1
|
|
|
versiondate |
date |
NOT NULL
DEFAULT ('now'::text)::date
|
|
|
annotationchanged |
boolean |
DEFAULT false
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryversiongeneral
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_EntryVersionParent_annotationChanged_true *
core.entryversionparent Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
NOT NULL
|
|
|
version |
integer |
NOT NULL
DEFAULT 1
|
|
|
versiondate |
date |
NOT NULL
DEFAULT ('now'::text)::date
|
|
|
annotationchanged |
boolean |
DEFAULT false
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryversionparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_EntryXrefDB_annotationChanged *
* Applied Rules: Rule_EntryXrefDB_annotationChanged_ins and _del *
core.entryxrefdb Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
core.xrefdb.xrefdbcode
|
xrefdbcode |
integer |
UNIQUE#1
NOT NULL
|
|
|
xrefprimaryidentifier |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryxrefdb
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_EntryXrefDB_no_dynamic_redundancy *
core.entryxrefdbdynamic Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
core.xrefdbdynamic.xrefdbcode
|
xrefdbcode |
integer |
UNIQUE#1
NOT NULL
|
|
|
xrefprimaryidentifier |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryxrefdbdynamic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.entryxrefdbparent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
xrefdbcode |
integer |
|
|
|
xrefprimaryidentifier |
character varying(32) |
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.entryxrefdbparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.
core.enzymenomenclature Structure
| F-Key |
Name |
Type |
Description |
|
|
enzymecode |
character varying(16) |
UNIQUE#1
NOT NULL
|
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.enzymenomenclature Constraints
| Name |
Constraint |
| enzymenomenclature_enzymecode_check |
CHECK (((enzymecode)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)) |
Permissions which apply to core.enzymenomenclature
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
The Main Index is typically UniProt (Swiss-Prot/TrEMBL).
Sequence changes imply entry changes:
CHECK (uniProtSeqUpDate >= uniProtEntryUpDate), # not yet decided for Swiss-Prot <=> EBI/TrEMBL
CHECK (uniProtSeqUpVersion >= uniProtEntryUpVersion) # not yet decided for Swiss-Prot <=> EBI/TrEMBL
core.externalmainxrefdata Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
PRIMARY KEY
|
|
|
uniprotextractiondate |
date |
DEFAULT now()
|
|
|
uniprotac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
uniprotsecondaryac |
character varying(32)[] |
|
|
|
uniprotid |
character varying(32) |
|
|
|
uniprotversion |
numeric(5,2) |
|
|
|
uniprotentryincorporateddate |
date |
|
|
|
uniprotsequpdate |
date |
|
|
|
uniprotsequpversion |
smallint |
|
|
|
uniprotentryupdate |
date |
|
|
|
uniprotentryupversion |
smallint |
|
|
|
uniprotdescription |
text |
|
|
|
uniprotenzymecode |
character varying(16) |
|
|
|
uniprotgenenames |
character varying(1024) |
|
|
|
uniprotorganelleplasmid |
character varying(256) |
|
|
|
uniprotcategorykeywords |
character varying(1024) |
|
|
|
uniprotxrefs |
character varying(1024)[] |
|
|
|
sportrembl |
boolean |
DEFAULT true
Swiss-Prot or TrEMBL? true => Swiss-Prot, false => TrEMBL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.externalmainxrefdata Constraints
| Name |
Constraint |
| externalmainxrefdata_check |
CHECK (((uniprotversion IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check1 |
CHECK (((uniprotsequpdate IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check10 |
CHECK (((uniprotxrefs IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check2 |
CHECK (((uniprotsequpversion IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check3 |
CHECK (((uniprotentryupdate IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check4 |
CHECK (((uniprotentryupversion IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check5 |
CHECK (((uniprotdescription IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check6 |
CHECK (((uniprotenzymecode IS NULL) OR ((uniprotac IS NOT NULL) AND ((uniprotenzymecode)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)))) |
| externalmainxrefdata_check7 |
CHECK (((uniprotgenenames IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check8 |
CHECK (((uniprotorganelleplasmid IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_check9 |
CHECK (((uniprotcategorykeywords IS NULL) OR (uniprotac IS NOT NULL))) |
| externalmainxrefdata_uniprotac_check |
CHECK ((uniprotac IS NOT NULL)) |
Permissions which apply to core.externalmainxrefdata
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Gel description will be restructed according to the forthcoming PSI recomandations -
No multiple image sets scanned from one gel and analyzed separately, or merged together for one master image, is within this structure yet! (to do: consider image sets)
* Applied Trigger: Trigger_Gel_shortName_melanieID *
* Applied Trigger: Trigger_Gel_showFlagSwitchTrue *
core.gel Structure
| F-Key |
Name |
Type |
Description |
|
|
gelid |
serial |
PRIMARY KEY
|
|
|
melaniegeneratedid |
character varying(64) |
UNIQUE
|
|
|
shortname |
character varying(32) |
UNIQUE
NOT NULL
|
|
|
fullname |
character varying(256) |
|
|
|
dimension |
smallint |
DEFAULT 2
|
|
|
startmw |
bigint |
|
|
|
endmw |
bigint |
|
|
|
startpi |
numeric(4,2) |
|
|
|
endpi |
numeric(4,2) |
|
|
core.organism.organismid
|
organismid |
integer |
NOT NULL
|
|
|
organismstrain |
character varying(256) |
|
|
core.gel.gelid
|
gelparentid |
integer |
Caution: this will imply an additional reference to preparation, causing a possible reference to another Analyte! (to be restructed)
|
|
core.gelpreparation.gelpreparationid
|
gelpreparationid |
integer |
Should be "Not NULL", but is not for more flexibility
|
|
core.gelinformatics.gelinformaticsid
|
gelinformaticsid |
integer |
Should be "Not NULL", but is not for more flexibility
|
|
core.biosourceinformation.biosourceinformationid
|
biosourceinformationid |
integer |
Set for flexibility (organism is redundant)
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.gel Constraints
| Name |
Constraint |
| gel_check |
CHECK ((endmw >= startmw)) |
| gel_check1 |
CHECK ((endpi >= startpi)) |
| gel_dimension_check |
CHECK (((dimension = 1) OR (dimension = 2))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.gel
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Reserved for computable map positions on remote databases
core.gelcomputabledynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
databasename |
character varying(64) |
NOT NULL
|
|
|
gelshortname |
character varying(32) |
NOT NULL
|
|
|
gelfullname |
character varying(256) |
|
|
|
organismspecies |
text |
|
|
|
taxonomycode |
integer |
|
|
|
gelcomputableurl |
text |
NOT NULL
URL with arguments is sent from ExPASy as a signal with params __MAP__ and __AC__
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.gelcomputabledynamic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.geldynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
databasename |
character varying(64) |
NOT NULL
|
|
|
gelshortname |
character varying(32) |
NOT NULL
|
|
|
gelfullname |
character varying(256) |
|
|
|
organismspecies |
text |
|
|
|
taxonomycode |
integer |
|
|
|
tissuename |
character varying(256) |
|
|
|
tissuespname |
character varying(256) |
|
|
|
gelurl |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.geldynamic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.gelimage Structure
| F-Key |
Name |
Type |
Description |
|
core.gel.gelid
|
gelid |
serial |
PRIMARY KEY
|
|
|
masterimage |
oid |
|
|
|
imageurl |
text |
|
|
|
imagepath |
text |
|
|
|
imagetype |
character varying(3) |
DEFAULT 'jpg'::character varying
|
|
|
smallimageurl |
text |
|
|
|
smallimagepath |
text |
|
|
|
smallimagetype |
character varying(3) |
DEFAULT 'jpg'::character varying
|
|
|
xpixelsize |
smallint |
|
|
|
ypixelsize |
smallint |
|
|
|
xratio |
numeric(6,4) |
NOT NULL
DEFAULT 1.0
xRatio and yRatio are < 1 if the displayed image has a smaller size than the original/reference image
|
|
|
yratio |
numeric(6,4) |
NOT NULL
DEFAULT 1.0
|
|
|
xpixelshift |
smallint |
|
|
|
ypixelshift |
smallint |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.gelimage Constraints
| Name |
Constraint |
| gelimage_xpixelsize_check |
CHECK ((xpixelsize >= 0)) |
| gelimage_ypixelsize_check |
CHECK ((ypixelsize >= 0)) |
Permissions which apply to core.gelimage
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Gel acquisition/informatics refers here to techniques not analysis, this will be restructed according to the forthcoming PSI recomandations
core.gelinformatics Structure
| F-Key |
Name |
Type |
Description |
|
|
gelinformaticsid |
serial |
PRIMARY KEY
|
|
|
uri |
character varying(4096) |
This may include URLs to local or external gel informatics documents (e.g. "PSI::MIAPE")
|
|
|
informaticsdocument |
text |
|
|
|
informaticsdescription |
text |
|
|
|
soft |
text |
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.gelinformatics
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
The Gel design will be highly restructed according to the forthcoming PSI recomandations!!
core.gelpreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
gelpreparationid |
serial |
PRIMARY KEY
|
|
core.analyte.analyteid
|
analyteid |
integer |
|
|
|
uri |
character varying(4096) |
This may include URLs to local or external gel preparation protocols (e.g. "PSI::MIAPE")
|
|
|
preparationdocument |
text |
|
|
|
preparationdescription |
text |
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.gelpreparation
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_GelTissueSP_uc *
core.geltissuesp Structure
| F-Key |
Name |
Type |
Description |
|
core.gel.gelid
|
gelid |
integer |
UNIQUE#1
|
|
core.tissuesp.tissuespname
|
tissuespname |
character varying(256) |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.geltissuesp
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.genename Structure
| F-Key |
Name |
Type |
Description |
|
|
geneid |
serial |
PRIMARY KEY
|
|
|
genename |
character varying(16) |
UNIQUE#1
NOT NULL
|
|
core.organism.organismid
|
organismid |
integer |
UNIQUE#1
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.genename
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.geneontologyparent Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
NOT NULL
|
|
|
goid |
character varying(32) |
NOT NULL
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
Synchronise with EnzymeNomenclature
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.geneontologyparent Constraints
| Name |
Constraint |
| geneontologyparent_mappedenzymeclassification_check |
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)) |
Permissions which apply to core.geneontologyparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.geneorderedlocus Structure
| F-Key |
Name |
Type |
Description |
|
core.genename.geneid
|
geneid |
integer |
UNIQUE#1
NOT NULL
|
|
|
orderedlocusname |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.geneorderedlocus
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.geneorf Structure
| F-Key |
Name |
Type |
Description |
|
core.genename.geneid
|
geneid |
integer |
UNIQUE#1
NOT NULL
|
|
|
orfname |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.geneorf
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.generaltopicdefinition Structure
| F-Key |
Name |
Type |
Description |
|
|
generaltopicid |
serial |
PRIMARY KEY
|
|
|
topicname |
character varying(64) |
UNIQUE
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.generaltopicdefinition
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.generaltopicentrydata Structure
| F-Key |
Name |
Type |
Description |
|
|
topicdataid |
serial |
PRIMARY KEY
|
|
core.generaltopicdefinition.generaltopicid
|
generaltopicid |
integer |
|
|
|
topicdatatext |
text |
|
|
|
allreferences |
integer[] |
|
|
|
ambiguousreference |
boolean |
DEFAULT false
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.generaltopicentrydata Constraints
| Name |
Constraint |
| generaltopicentrydata_check |
CHECK ((((ambiguousreference = false) AND (allreferences[1] IS NOT NULL)) OR ((ambiguousreference = true) AND (allreferences[1] IS NULL)))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.generaltopicentrydata
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.genesynonym Structure
| F-Key |
Name |
Type |
Description |
|
core.genename.geneid
|
geneid |
integer |
UNIQUE#1
NOT NULL
|
|
|
synonym |
character varying(16) |
UNIQUE#1
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.genesynonym
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.journal Structure
| F-Key |
Name |
Type |
Description |
|
|
journalid |
serial |
PRIMARY KEY
|
|
|
journalname |
character varying(256) |
UNIQUE
NOT NULL
|
|
|
url |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.journal
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
To do: include a Trigger to check that for the "new" option, new version > max(version)
core.make2ddbtool Structure
| F-Key |
Name |
Type |
Description |
|
|
version |
numeric(4,2) |
NOT NULL
DEFAULT 0.0
|
|
|
subversion |
character varying(64) |
|
|
|
versiondate |
date |
|
|
|
postgresqlversion |
text |
|
|
|
action |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.make2ddbtool Constraints
| Name |
Constraint |
| make2ddbtool_action_check |
CHECK (((("action" = 'create'::text) OR ("action" = 'transform'::text)) OR ("action" = 'update'::text))) |
Permissions which apply to core.make2ddbtool
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.mappingtopicdefinition Structure
| F-Key |
Name |
Type |
Description |
|
|
mappingtechnique |
character varying(8) |
PRIMARY KEY
|
|
|
techniquedescription |
character varying(256) |
|
|
|
containingregexp |
text |
NOT NULL
|
|
|
excludingregexp |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.mappingtopicdefinition
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.molecularfunction Structure
| F-Key |
Name |
Type |
Description |
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goid |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.molecularfunction Constraints
| Name |
Constraint |
| geneontologyparent_mappedenzymeclassification_check |
CHECK (((mappedenzymeclassification)::text ~ '^[0-9](.([0-9]+|-)){3}$'::text)) |
Permissions which apply to core.molecularfunction
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
We will define a more precise way to describe strains, etc.. -> organism.
For the moment, strains can be described - additionaly - at the BioSource or the Gel level.
core.organism Structure
| F-Key |
Name |
Type |
Description |
|
|
organismid |
serial |
PRIMARY KEY
|
|
|
organismspecies |
text |
UNIQUE
NOT NULL
|
|
|
organismclassification |
text |
NOT NULL
|
|
core.xrefdb.xrefdbcode
|
taxonomyxrefdbcode |
integer |
UNIQUE#1
|
|
|
taxonomycode |
integer |
UNIQUE#1
For several strains: for the moment use a double NULL pair, or use some personal taxonomyXref DB.
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.organism
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.project Structure
| F-Key |
Name |
Type |
Description |
|
|
projectid |
serial |
PRIMARY KEY
|
|
|
description |
text |
|
|
|
uri |
character varying(4096) |
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.project
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.reference Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
serial |
PRIMARY KEY
|
|
core.referencework.referenceworkid
|
referenceworkid |
integer |
|
|
|
referencetitle |
text |
|
|
core.referencetype.referencetypeid
|
referencetypeid |
integer |
NOT NULL
DEFAULT 1
|
|
|
referencechecksum |
character(16) |
UNIQUE
NOT NULL
Update with views or skip? (deprecated)
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.reference
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Spots experimental References are integrated within the spots experimental Tables.
core.referencedentry Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
|
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
PRIMARY KEY
|
|
|
rndisplayedvalue |
smallint |
UNIQUE#1
DEFAULT 1
This field is kept for compatibility/historical purpose
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencedentry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencedgel Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
|
|
core.gel.gelid
|
gelid |
integer |
PRIMARY KEY
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencedgel
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencedobjectparent Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencedobjectparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencedproject Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
|
|
core.project.projectid
|
projectid |
integer |
PRIMARY KEY
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencedproject
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencedsample Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
|
|
core.sample.sampleid
|
sampleid |
integer |
PRIMARY KEY
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencedsample
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationbook Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationbook_referenceid_seq'::regclass)
|
|
core.book.bookid
|
bookid |
integer |
NOT NULL
|
|
|
volume |
smallint |
|
|
|
pagefirst |
integer |
NOT NULL
|
|
|
pagelast |
integer |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationbook Constraints
| Name |
Constraint |
| referencelocationbook_check |
CHECK (((pagelast >= pagefirst) AND (pagefirst > 0))) |
| referencelocationbook_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'Book'::character varying) = true)) |
Permissions which apply to core.referencelocationbook
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationjournal Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationjournal_referenceid_seq'::regclass)
|
|
core.journal.journalid
|
journalid |
integer |
NOT NULL
|
|
|
volume |
smallint |
NOT NULL
|
|
|
subvolume |
smallint |
|
|
|
pagefirst |
integer |
NOT NULL
|
|
|
pagelast |
integer |
NOT NULL
|
|
|
year |
smallint |
NOT NULL
|
|
|
crossreferences |
character varying(128)[] |
|
|
|
unpublished |
boolean |
DEFAULT false
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationjournal Constraints
| Name |
Constraint |
| referencelocationjournal_check |
CHECK ((((pagelast >= pagefirst) AND (pagefirst > 0)) OR ((pagefirst = 0) AND (pagelast = 0)))) |
| referencelocationjournal_referenceid_check |
CHECK (((common.make2db_rl_verify_type(referenceid, 'Journal'::character varying) = true) OR (common.make2db_rl_verify_type(referenceid, 'Unpublished results'::character varying) = true))) |
| referencelocationjournal_subvolume_check |
CHECK ((subvolume >= 0)) |
| referencelocationjournal_volume_check |
CHECK ((volume >= 0)) |
| referencelocationjournal_year_check |
CHECK (("year" >= 0)) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.referencelocationjournal
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationother Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationother_referenceid_seq'::regclass)
|
|
|
text |
text |
NOT NULL
|
|
|
personalcomment |
character varying(256) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationother Constraints
| Name |
Constraint |
| referencelocationother_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'OTHER'::character varying) = true)) |
Permissions which apply to core.referencelocationother
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationparent Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
serial |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.referencelocationparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationpatent Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationpatent_referenceid_seq'::regclass)
|
|
|
patent_publication_number |
character varying(16) |
NOT NULL
|
|
|
date |
date |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationpatent Constraints
| Name |
Constraint |
| referencelocationpatent_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'Patent applications'::character varying) = true)) |
Permissions which apply to core.referencelocationpatent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationsubmission Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationsubmission_referenceid_seq'::regclass)
|
|
|
month |
smallint |
NOT NULL
|
|
|
year |
smallint |
NOT NULL
|
|
core.xrefdb.xrefdbcode
|
xrefdbcode |
integer |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationsubmission Constraints
| Name |
Constraint |
| referencelocationsubmission_month_check |
CHECK ((("month" > 0) AND ("month" < 13))) |
| referencelocationsubmission_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'Submitted'::character varying) = true)) |
| referencelocationsubmission_year_check |
CHECK (("year" > 0)) |
Permissions which apply to core.referencelocationsubmission
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationthesis Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationthesis_referenceid_seq'::regclass)
|
|
|
year |
smallint |
NOT NULL
|
|
|
institution |
character varying(128) |
NOT NULL
|
|
|
country |
character varying(64) |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationthesis Constraints
| Name |
Constraint |
| referencelocationthesis_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'Thesis'::character varying) = true)) |
| referencelocationthesis_year_check |
CHECK (("year" > 0)) |
Permissions which apply to core.referencelocationthesis
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencelocationunpubobservations Structure
| F-Key |
Name |
Type |
Description |
|
core.reference.referenceid
|
referenceid |
integer |
PRIMARY KEY
DEFAULT nextval('referencelocationunpubobservations_referenceid_seq'::regclass)
|
|
|
month |
smallint |
NOT NULL
|
|
|
year |
smallint |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.referencelocationunpubobservations Constraints
| Name |
Constraint |
| referencelocationunpubobservations_month_check |
CHECK ((("month" > 0) AND ("month" < 13))) |
| referencelocationunpubobservations_referenceid_check |
CHECK ((common.make2db_rl_verify_type(referenceid, 'Unpublished observations'::character varying) = true)) |
| referencelocationunpubobservations_year_check |
CHECK (("year" > 0)) |
Permissions which apply to core.referencelocationunpubobservations
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencetype Structure
| F-Key |
Name |
Type |
Description |
|
|
referencetypeid |
serial |
PRIMARY KEY
|
|
|
referencetype |
character varying(32) |
UNIQUE
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.referencetype
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.referencework Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceworkid |
serial |
PRIMARY KEY
|
|
|
referenceworkdescription |
character varying(64) |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.referencework
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.release Structure
| F-Key |
Name |
Type |
Description |
|
|
releasenum |
integer |
PRIMARY KEY
|
|
|
subrelease |
smallint |
PRIMARY KEY
DEFAULT 1
|
|
|
releasedate |
date |
NOT NULL
DEFAULT ('now'::text)::date
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.release
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Consider merging Sample and SamplePreparation, or rename the latter to SamplePreparationProtocol
core.sample Structure
| F-Key |
Name |
Type |
Description |
|
|
sampleid |
serial |
PRIMARY KEY
|
|
core.biosource.biosourceid
|
biosourceid |
integer |
Should be "Not NULL", but is not for more flexibility
|
|
|
uri |
character varying(4096) |
|
|
core.samplepreparation.samplepreparationid
|
samplepreparationid |
integer |
|
|
|
description |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.sample
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.samplepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
samplepreparationid |
serial |
PRIMARY KEY
|
|
|
uri |
character varying(4096) |
|
|
|
samplepreparationdocument |
text |
|
|
|
samplepreparationprotocol |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.samplepreparation
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.secondaryac Structure
| F-Key |
Name |
Type |
Description |
|
|
secondaryac |
character varying(32) |
NOT NULL
|
|
core.entry.ac
|
ac |
character varying(32) |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.secondaryac
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
UNIQUE (mw, pI, gelID) and UNIQUE (xCoordinate, yCoordiante, gelID) constraints have not been added.
* Applied Trigger: Trigger_Spot_insert *
core.spot Structure
| F-Key |
Name |
Type |
Description |
|
|
spotid |
character varying(16) |
PRIMARY KEY
|
|
core.gel.gelid
|
gelid |
integer |
PRIMARY KEY
|
|
|
mw |
integer |
NOT NULL
By convention, set to -1 for large-scale non-identified spots
|
|
|
pi |
numeric(4,2) |
By convention, set to -1.00 for large-scale non-identified spots
|
|
|
xcoordinate |
integer |
|
|
|
ycoordinate |
integer |
|
|
|
odrelative |
real |
|
|
|
volumerelative |
real |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spot
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotdataaacid Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
PRIMARY KEY
DEFAULT nextval('spotdataaacid_dataexpid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
core.spot.spotid#1
|
spotid |
character varying(16) |
PRIMARY KEY
|
|
core.spot.gelid#1
|
gelid |
integer |
PRIMARY KEY
|
|
core.reference.referenceid
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
aminoacidlist |
text |
NOT NULL
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotdataaacid Constraints
| Name |
Constraint |
| spotdataparent_appreciation_check |
CHECK (((appreciation > 0) AND (appreciation < 11))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotdataaacid
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotdataother Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
PRIMARY KEY
DEFAULT nextval('spotdataother_dataexpid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
core.spot.spotid#1
|
spotid |
character varying(16) |
PRIMARY KEY
|
|
core.spot.gelid#1
|
gelid |
integer |
PRIMARY KEY
|
|
core.reference.referenceid
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
results |
text |
NOT NULL
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotdataother Constraints
| Name |
Constraint |
| spotdataparent_appreciation_check |
CHECK (((appreciation > 0) AND (appreciation < 11))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotdataother
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_SpotDataParent_nextval_dataExpID *
* Applied Trigger: Trigger_SpotDataParent_showFlagSwitchTrue *
core.spotdataparent Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
serial |
NOT NULL
|
|
|
humanidentifier |
character varying(256) |
This field is to hold an identifier given by data producers to identify their data
experiment (different from the database generated dataExpID Primary Key, often a file name). It is not UNIQUE (e.g. for MS/MS file output
has a serie of spectra), and it may be NULL, as no such identifier is systematically given by users
|
|
core.spot.spotid#1
|
spotid |
character varying(16) |
|
|
core.spot.gelid#1
|
gelid |
integer |
|
|
core.reference.referenceid
|
referenceid |
integer |
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
This may include URLs to local or external experiment data/description files (e.g. "PSI::MzData")
|
|
|
datadocument |
text |
This may correspond in the sub-classes to, e.g., "PSI:mzData": give a files system path (no storage as large objects)
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotdataparent Constraints
| Name |
Constraint |
| spotdataparent_appreciation_check |
CHECK (((appreciation > 0) AND (appreciation < 11))) |
Permissions which apply to core.spotdataparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotdatapeptmassf Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
PRIMARY KEY
DEFAULT nextval('spotdatapeptmassf_dataexpid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
core.spot.spotid#1
|
spotid |
character varying(16) |
PRIMARY KEY
|
|
core.spot.gelid#1
|
gelid |
integer |
PRIMARY KEY
|
|
core.reference.referenceid
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
peptidemasses |
double precision[] |
NOT NULL
[mass][intensity]
|
|
|
enzyme |
character varying(32) |
NOT NULL
DEFAULT 'TRYPSIN'::character varying
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotdatapeptmassf Constraints
| Name |
Constraint |
| spotdataparent_appreciation_check |
CHECK (((appreciation > 0) AND (appreciation < 11))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotdatapeptmassf
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotdatatandemms Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
PRIMARY KEY
DEFAULT nextval('spotdatatandemms_dataexpid_seq'::regclass)
dataExpID combined with gelID and AC -> we can trace back the corresponding parent peptide origin from the SpotDataPeptMassF table
|
|
|
humanidentifier |
character varying(256) |
|
|
core.spot.spotid#1
|
spotid |
character varying(16) |
PRIMARY KEY
|
|
core.spot.gelid#1
|
gelid |
integer |
PRIMARY KEY
|
|
core.reference.referenceid
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
parentmass |
double precision |
|
|
|
parentcharge |
smallint |
|
|
|
ionmasses |
double precision[] |
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotdatatandemms Constraints
| Name |
Constraint |
| spotdataparent_appreciation_check |
CHECK (((appreciation > 0) AND (appreciation < 11))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotdatatandemms
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_SpotEntry_showFlagSwitchTrue *
core.spotentry Structure
| F-Key |
Name |
Type |
Description |
|
core.spot.spotid#1
|
spotid |
character varying(16) |
UNIQUE#1
|
|
core.spot.gelid#1
|
gelid |
integer |
UNIQUE#1
|
|
core.entry.ac
|
ac |
character varying(32) |
UNIQUE#1
NOT NULL
|
|
|
fragment |
boolean |
DEFAULT false
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotentry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Permissions which apply to core.spotentrygeneraltopic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotentrymappingtopic Structure
| F-Key |
Name |
Type |
Description |
|
core.generaltopicentrydata.topicdataid
|
topicdataid |
integer |
NOT NULL
|
|
core.spotentry.spotid#1
|
spotid |
character varying(16) |
|
|
core.spotentry.gelid#1
|
gelid |
integer |
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
mappingtechnique |
character varying(8)[] |
DEFAULT '{N/A}'::character varying[]
A Check function verify reference to MappingTopicDefinition
(Should add a Trigger that updates values if definition changes)
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotentrymappingtopic Constraints
| Name |
Constraint |
| spotentrymappingtopic_mappingtechnique_check |
CHECK (common.make2db_verify_mappingtechnique(mappingtechnique)) |
Permissions which apply to core.spotentrymappingtopic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Permissions which apply to core.spotentrytopicparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotidentificationaacid Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
integer |
PRIMARY KEY
DEFAULT nextval('spotidentificationaacid_identificationid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
|
hassubset |
boolean |
DEFAULT false
|
|
core.spotdataaacid.dataexpid#2
|
dataexpid |
integer |
|
|
core.spotdataaacid.spotid#2
core.spotentry.spotid#1
|
spotid |
character varying(16) |
NOT NULL
|
|
core.spotdataaacid.gelid#2
core.spotentry.gelid#1
|
gelid |
integer |
NOT NULL
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
isoform |
text |
|
|
|
version |
integer |
DEFAULT 1
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
identificationdocument |
text |
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
DEFAULT true
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
aminoacidlist |
text |
NOT NULL
(In theory) ensure the amino acids subset is equal to the whole SpotDataAAcid.aminoAcidList
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationaacid Constraints
| Name |
Constraint |
| spotidentificationaacid_hassubset_check |
CHECK ((hassubset = false)) |
| spotidentificationparent_appreciation_check |
CHECK (((appreciation > (0)::numeric) AND (appreciation < (10)::numeric))) |
Permissions which apply to core.spotidentificationaacid
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotidentificationother Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
integer |
PRIMARY KEY
DEFAULT nextval('spotidentificationother_identificationid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
|
hassubset |
boolean |
DEFAULT false
|
|
core.spotdataother.dataexpid#2
|
dataexpid |
integer |
|
|
core.spotdataother.spotid#2
core.spotentry.spotid#1
|
spotid |
character varying(16) |
NOT NULL
|
|
core.spotdataother.gelid#2
core.spotentry.gelid#1
|
gelid |
integer |
NOT NULL
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
isoform |
text |
|
|
|
version |
integer |
DEFAULT 1
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
identificationdocument |
text |
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
DEFAULT true
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
results |
text |
NOT NULL
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationother Constraints
| Name |
Constraint |
| spotidentificationother_hassubset_check |
CHECK ((hassubset = false)) |
| spotidentificationparent_appreciation_check |
CHECK (((appreciation > (0)::numeric) AND (appreciation < (10)::numeric))) |
Permissions which apply to core.spotidentificationother
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_SpotIdentificationParent_nextval_identificationID *
* Applied Trigger: Trigger_SpotIdentificationParent_showFlagSwitchTrue *
SpotID and GelID are needed, as DataParent may miss!
core.spotidentificationparent Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
serial |
NOT NULL
|
|
|
humanidentifier |
character varying(256) |
This field is to hold an identifier given by data analyzers to identify
a specific identification (different from the database generated identificationID Primary Key). It is NOT UNIQUE (as the same analysis
may refer to several identified proteins). It may be NULL, as no such identifier is systematically given by users
|
|
|
hassubset |
boolean |
DEFAULT false
|
|
|
dataexpid |
integer |
|
|
core.spotentry.spotid#1
|
spotid |
character varying(16) |
NOT NULL
|
|
core.spotentry.gelid#1
|
gelid |
integer |
NOT NULL
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
isoform |
text |
Check for forthcoming annotations of varsplices, variants and conflicts according to UniProt
|
|
|
version |
integer |
DEFAULT 1
This field version corresponds idealy to the identified entry (new) version when the identification has been performed
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
This may include URLs to local or external identification description files (e.g. "PSI::AnalysisXML")
|
|
|
identificationdocument |
text |
This may correspond in the sub-classes to, e.g., "PSI:AnalysisXML": give a file system path (no storage as large objects)
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
DEFAULT true
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationparent Constraints
| Name |
Constraint |
| spotidentificationparent_appreciation_check |
CHECK (((appreciation > (0)::numeric) AND (appreciation < (10)::numeric))) |
Permissions which apply to core.spotidentificationparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotidentificationpeptmassf Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
integer |
PRIMARY KEY
DEFAULT nextval('spotidentificationpeptmassf_identificationid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
|
hassubset |
boolean |
DEFAULT false
|
|
core.spotdatapeptmassf.dataexpid#2
|
dataexpid |
integer |
|
|
core.spotdatapeptmassf.spotid#2
core.spotentry.spotid#1
|
spotid |
character varying(16) |
NOT NULL
|
|
core.spotdatapeptmassf.gelid#2
core.spotentry.gelid#1
|
gelid |
integer |
NOT NULL
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
isoform |
text |
|
|
|
version |
integer |
DEFAULT 1
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
identificationdocument |
text |
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
DEFAULT true
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
peptidemasses |
double precision[] |
NOT NULL
[mass][intensity];
(In theory) ensure this is a subset of SpotDataPeptMassF.peptideMasses
|
|
|
relateddata |
text |
|
|
|
xxac |
character varying(32) |
The "xx" fields are specific to SWISS-2DPAGE
|
|
|
xxdirectory |
character varying(256) |
|
|
|
xxfile |
character varying(64) |
|
|
|
xxprogversion |
character varying(64) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationpeptmassf Constraints
| Name |
Constraint |
| spotidentificationparent_appreciation_check |
CHECK (((appreciation > (0)::numeric) AND (appreciation < (10)::numeric))) |
| spotidentificationpeptmassf_hassubset_check |
CHECK ((hassubset = false)) |
Permissions which apply to core.spotidentificationpeptmassf
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
This identification category has a Subset of identified elements
core.spotidentificationtandemms Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
integer |
PRIMARY KEY
DEFAULT nextval('spotidentificationtandemms_identificationid_seq'::regclass)
|
|
|
humanidentifier |
character varying(256) |
|
|
|
hassubset |
boolean |
DEFAULT false
hasSubset is true for TandemMS
|
|
core.spotdatatandemms.dataexpid#2
|
dataexpid |
integer |
|
|
core.spotdatatandemms.spotid#2
core.spotentry.spotid#1
|
spotid |
character varying(16) |
NOT NULL
|
|
core.spotdatatandemms.gelid#2
core.spotentry.gelid#1
|
gelid |
integer |
NOT NULL
|
|
core.spotentry.ac#1
|
ac |
character varying(32) |
|
|
|
isoform |
text |
|
|
|
version |
integer |
DEFAULT 1
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
identificationdocument |
text |
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
DEFAULT true
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
NOT NULL
DEFAULT true
|
|
|
showflagswitch |
boolean |
NOT NULL
DEFAULT true
|
|
|
ionmasses |
double precision[] |
[mass][intensity];
(In theory) ensure this is a subset of SpotDataTandemMS.ionMasses
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationtandemms Constraints
| Name |
Constraint |
| spotidentificationparent_appreciation_check |
CHECK (((appreciation > (0)::numeric) AND (appreciation < (10)::numeric))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.spotidentificationtandemms
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.spotidentificationtandemmssubset Structure
| F-Key |
Name |
Type |
Description |
|
core.spotidentificationtandemms.identificationid
|
identificationid |
integer |
NOT NULL
|
|
|
ionmasses |
double precision[] |
(In theory) ensure this is a subset of SpotIdentificationTandemMS.ionMasses
|
|
|
identifiedpeptidesequence |
text |
NOT NULL
|
|
|
sequencestartposition |
smallint |
|
|
|
sequenceendposition |
smallint |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.spotidentificationtandemmssubset Constraints
| Name |
Constraint |
| spotidentificationtandemmssubset_check |
CHECK ((sequenceendposition >= sequencestartposition)) |
Permissions which apply to core.spotidentificationtandemmssubset
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.study Structure
| F-Key |
Name |
Type |
Description |
|
|
studyid |
serial |
PRIMARY KEY
|
|
core.project.projectid
|
projectid |
integer |
|
|
|
description |
text |
|
|
core.contact.contactid
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.study
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.studygroup Structure
| F-Key |
Name |
Type |
Description |
|
|
studygroupid |
serial |
PRIMARY KEY
|
|
core.study.studyid
|
studyid |
integer |
NOT NULL
|
|
|
description |
text |
|
|
core.biosourceinformation.biosourceinformationid
|
biosourceinformationid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.studygroup
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Expecting a forthcoming PSI proposition, probably based on a hierarchical onthology
core.tissue Structure
| F-Key |
Name |
Type |
Description |
|
|
tissueid |
serial |
PRIMARY KEY
|
|
|
tissuename |
character varying(256) |
NOT NULL
|
|
core.tissue.tissueid
|
tissueparentid |
integer |
|
|
|
tissuecomment |
character varying(1024) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.tissue
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
TissueSP is a very general designation of the cell organ/tissue/liquid as proposed by Swiss-Prot...
Not to be edited by users! the tisslist.list is part of the package, it can be automatically loaded from the ExPASy server (the SWISS-PROT tisslist.txt).
Recently a new Swiss-Prot identifier has been defined, tissueSPName is used as a unique identifier for the moment!
Mapping with the Tissue table is expected in the future.
* Applied Trigger: Trigger_TissueSP_uc *
core.tissuesp Structure
| F-Key |
Name |
Type |
Description |
|
|
tissuespname |
character varying(256) |
PRIMARY KEY
|
|
|
tissuespdisplayedname |
character varying(256) |
NOT NULL
|
|
|
tissueindate |
date |
NOT NULL
DEFAULT '2006-06-27'::date
|
|
|
tissuecomment |
character varying(1024) |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.tissuesp
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_TissueSPAliase_uc *
core.tissuespaliase Structure
| F-Key |
Name |
Type |
Description |
|
core.tissuesp.tissuespname
|
tissuespname |
character varying(256) |
NOT NULL
|
|
|
alias |
character varying(256) |
NOT NULL
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.tissuespaliase
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_TissueSPTissueMapping_uc *
core.tissuesptissuemapping Structure
| F-Key |
Name |
Type |
Description |
|
core.tissuesp.tissuespname
|
tissuespname |
character varying(256) |
|
|
core.tissue.tissueid
|
tissueid |
integer |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.tissuesptissuemapping
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.tmp_last_entry Structure
| F-Key |
Name |
Type |
Description |
|
|
identifier |
character varying(32) |
|
|
|
id_method |
character varying(48) |
|
|
|
accession_number |
character varying(32) |
|
|
|
secondary_identifiers |
text |
|
|
|
creation |
text |
|
|
|
version_2d |
text |
|
|
|
version_general |
text |
|
|
|
description |
text |
|
|
|
genes |
text |
|
|
|
organism |
text |
|
|
|
organism_classification |
text |
|
|
|
taxonomy_cross_reference |
text |
|
|
|
masters |
text |
|
|
|
images |
text |
|
|
|
free_comments |
text |
|
|
|
reference_lines |
text |
|
|
|
one_d_comments |
text |
|
|
|
one_d_blocks |
text |
|
|
|
two_d_comments |
text |
|
|
|
two_d_blocks |
text |
|
|
|
database_cross_reference |
text |
|
Permissions which apply to core.tmp_last_entry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.viewentry Structure
| F-Key |
Name |
Type |
Description |
|
|
identifier |
character varying(32) |
|
|
|
id_method |
character varying(48) |
|
|
|
accession_number |
character varying(32) |
|
|
|
secondary_identifiers |
text |
|
|
|
creation |
text |
|
|
|
version_2d |
text |
|
|
|
version_general |
text |
|
|
|
description |
text |
|
|
|
genes |
text |
|
|
|
organism |
text |
|
|
|
organism_classification |
text |
|
|
|
taxonomy_cross_reference |
text |
|
|
|
masters |
text |
|
|
|
images |
text |
|
|
|
free_comments |
text |
|
|
|
reference_lines |
text |
|
|
|
one_d_comments |
text |
|
|
|
one_d_blocks |
text |
|
|
|
two_d_comments |
text |
|
|
|
two_d_blocks |
text |
|
|
|
database_cross_reference |
text |
|
Permissions which apply to core.viewentry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.viewmapentrylist Structure
| F-Key |
Name |
Type |
Description |
|
|
gelid |
integer |
|
|
|
genes |
character varying(1024) |
|
|
|
description |
text |
|
|
|
spotid |
character varying(16) |
|
|
|
ac |
character varying(32) |
|
|
|
id |
character varying(32) |
|
|
|
pi |
numeric(4,2) |
|
|
|
mw |
numeric(6,3) |
|
|
|
volumerelative |
real |
|
|
|
odrelative |
real |
|
|
|
fragment |
boolean |
|
|
|
topicdescription |
text |
|
|
|
mappingtechniques |
text |
|
|
|
availableresults |
text |
|
|
|
rn_references |
text |
|
|
|
referenceids |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
Permissions which apply to core.viewmapentrylist
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.viewref Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
referenceworkdescription |
character varying(64) |
|
|
|
crossreferences |
character varying(256) |
|
|
|
authorsgroup |
character varying(2048) |
|
|
|
authors |
character varying(8192) |
|
|
|
referencetitle |
text |
|
|
|
referencelocation |
text |
|
Permissions which apply to core.viewref
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.viewspotentry Structure
| F-Key |
Name |
Type |
Description |
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
fragment |
boolean |
|
|
|
aminoacidlist |
text |
Specific data sets are separated by
|
|
|
aa_version |
integer |
|
|
|
msms |
text |
Specific data sets are separated by
|
|
|
ms_version |
integer |
|
|
|
peptidesequences |
text |
Specific data sets are separated by
|
|
|
peptseq_version |
integer |
|
|
|
peptidemasses |
text |
Specific data sets are separated by
|
|
|
pmf_version |
integer |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
Permissions which apply to core.viewspotentry
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)
core.viewspotentrylast Structure
| F-Key |
Name |
Type |
Description |
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
fragment |
boolean |
|
|
|
aminoacidlist |
text |
|
|
|
aa_version |
integer |
|
|
|
msms |
text |
|
|
|
ms_version |
integer |
|
|
|
peptidesequences |
text |
|
|
|
peptseq_version |
integer |
|
|
|
peptidemasses |
text |
|
|
|
pmf_version |
integer |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
Permissions which apply to core.viewspotentrylast
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
* Applied Trigger: Trigger_XrefDB_insensitiveName *
core.xrefdb Structure
| F-Key |
Name |
Type |
Description |
|
|
xrefdbcode |
integer |
PRIMARY KEY
DEFAULT nextval('xrefdb_xrefdbcode_seq'::regclass)
|
|
|
xrefdbname |
character varying(64) |
UNIQUE
NOT NULL
|
|
|
description |
text |
|
|
|
url |
text |
|
|
|
displayerurl |
text |
|
|
|
displayerparameters |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
core.xrefdb Constraints
| Name |
Constraint |
| xrefdb_check |
CHECK (((((((xrefdbcode > 5) OR ((xrefdbcode = 1) AND ((xrefdbname)::text ~* '^Swiss-?Prot$'::text))) OR ((xrefdbcode = 2) AND ((xrefdbname)::text ~* '^TrEMBL$'::text))) OR ((xrefdbcode = 3) AND ((xrefdbname)::text ~* '^SWISS-?2DPAGE$'::text))) OR ((xrefdbcode = 4) AND ((xrefdbname)::text ~* '^Swiss-?Prot:SRS$'::text))) OR ((xrefdbcode = 5) AND ((xrefdbname)::text ~* '^GO$'::text)))) |
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.xrefdb
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
By convention: any database not present in XrefDB has an XrefDBCode > 1000,
this is ensured by the update interface!
* Applied Trigger: Trigger_XrefDBDynamic_insensitiveName *
core.xrefdbdynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
xrefdbcode |
integer |
PRIMARY KEY
DEFAULT nextval('xrefdbdynamic_xrefdbcode_seq'::regclass)
|
|
|
xrefdbname |
character varying(64) |
UNIQUE
NOT NULL
|
|
|
description |
text |
|
|
|
url |
text |
|
|
|
displayerurl |
text |
|
|
|
displayerparameters |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Tables referencing this one via Foreign Key Constraints:
Permissions which apply to core.xrefdbdynamic
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
core.xrefdbparent Structure
| F-Key |
Name |
Type |
Description |
|
|
xrefdbcode |
serial |
NOT NULL
|
|
|
xrefdbname |
character varying(64) |
|
|
|
description |
text |
|
|
|
url |
text |
|
|
|
displayerurl |
text |
|
|
|
displayerparameters |
text |
|
|
|
userstamp |
character varying(128) |
DEFAULT "current_user"()
|
|
|
update |
timestamp without time zone |
DEFAULT now()
|
Permissions which apply to core.xrefdbparent
| User |
Select |
Insert |
Update |
Delete |
Reference |
Rule |
Trigger |
| mostaguir |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
♦ |
| select2d |
♦ |
|
|
|
|
|
|
Index -
Schema core
Returns: boolean
Language: PLPGSQL
FUNCTION TO DROP A VARIABLE CLASS
-- FUNCTION TO DROP A VARIABLE CLASS
------------------------------------
DECLARE
class_type ALIAS for $1;
class_name_init ALIAS for $2;
class_name VARCHAR(128);
class_table_init ALIAS for $3;
class_table VARCHAR(128);
BEGIN
-- !! Handle with EXTREME CARE !!
class_name = lower(class_name_init);
class_table = lower(class_table_init);
IF EXISTS (SELECT relname FROM pg_class WHERE relname = class_name::NAME)
THEN IF class_type = 'T' OR class_type = 't'
THEN EXECUTE 'DROP TABLE ' || class_name;
RETURN 'true';
ELSE IF class_type = 'V' OR class_type = 'v'
THEN EXECUTE 'DROP VIEW ' || class_name;
RETURN 'true';
ELSE IF class_type = 'I' OR class_type = 'i'
THEN EXECUTE 'DROP INDEX ' || class_name;
RETURN 'true';
ELSE IF class_type = 'R' OR class_type = 'r'
THEN EXECUTE 'DROP RULE ' || class_name;
RETURN 'true';
END IF;
END IF;
END IF;
END IF;
END IF;
IF EXISTS (SELECT tgname FROM pg_trigger WHERE tgname = class_name::NAME)
THEN IF class_type = 'G' OR class_type = 'g'
THEN EXECUTE 'DROP TRIGGER ' || class_name || ' ON ' || class_table;
RETURN 'true';
END IF;
END IF;
RETURN 'false';
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO DROP ALL NAMED FUNCTIONS (deprecated since postgreSQL 7.1 REPLACE command)
-- FUNCTION TO DROP ALL NAMED FUNCTIONS
---------------------------------------
DECLARE
function_name_init ALIAS for $1;
function_name VARCHAR(128);
my_record RECORD;
BEGIN
function_name = lower(function_name_init);
IF NOT EXISTS (SELECT pg_proc.OID AS proc_OID FROM pg_proc WHERE proname = function_name::NAME)
THEN RETURN 'false';
END IF;
FOR my_record IN
SELECT pg_proc.OID AS proc_OID FROM pg_proc
WHERE lower(proname) = function_name::NAME
LOOP
DELETE FROM pg_proc WHERE OID = my_record.proc_OID;
END LOOP;
RETURN 'true';
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO BACKUP OR RESTORE THE CURRENT VIEWS VIA TEMPORARY TABLES
-- FUNCTION TO BACKUP OR RESTORE THE CURRENT VIEWS VIA TEMPORARY TABLES
-----------------------------------------------------------------------
-- Argument: True -> Backup, False -> Restore
DECLARE
my_argument ALIAS FOR $1;
my_backup_view TEXT;
my_status BOOLEAN;
my_record RECORD;
BEGIN
my_status = FALSE;
IF (my_argument IS NULL) THEN RETURN my_status; END IF;
FOR my_record IN
SELECT tablename FROM pg_tables WHERE tablename ~* '^View' AND lower(schemaname) = 'core'
LOOP
my_backup_view := lower(my_record.tablename || '_backup');
IF (my_argument IS TRUE) THEN
my_status = TRUE;
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = my_backup_view) THEN
EXECUTE 'DROP TABLE ' || my_backup_view;
END IF;
EXECUTE 'CREATE TEMPORARY TABLE ' || my_backup_view || ' AS SELECT * FROM ' || my_record.tablename;
ELSE
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = my_backup_view) THEN
my_status = TRUE;
EXECUTE 'DELETE FROM ' || my_record.tablename;
EXECUTE 'INSERT INTO ' || my_record.tablename || ' SELECT * FROM ' || my_backup_view;
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION FOR ENTRY/IES "VIEWS" CONSTRUCTION
(Arguments: an entry accession number, or "all" to construct all entries)
-- FUNCTION FOR ENTRY/IES "VIEWS" CONSTRUCTION
----------------------------------------------
-- (Arguments: an entry accession number, or "all" to construct all entries)
DECLARE
my_ac ALIAS for $1;
my_limit_search_ac VARCHAR(32);
void_operation BOOLEAN;
my_record RECORD;
BEGIN
SET DATESTYLE TO 'POSTGRES, EUROPEAN';
void_operation := 'false';
IF my_ac = '' THEN RETURN 'false';
END IF;
RAISE NOTICE 'Entry construction in progress...';
IF my_ac = 'all'
THEN
RAISE NOTICE 'Analyzing tables...';
-- ANALYZE; -- KHM (server shuts down in mordor!!)
IF NOT (SELECT make2db_reunit_refs(0)) -- Construct General Reference Blocks in ViewRef -> general: (0)
THEN
RAISE NOTICE 'No result performing make2db_reunit_refs function on all entries. Entry construction is partially incomplete!
';
void_operation := 'true';
END IF;
IF NOT (SELECT make2db_reunit_spots('all')) -- Construct ACs 1D and 2D Blocks in ViewSpotEntry -> general:("all")
THEN
RAISE NOTICE 'No result performing make2db_reunit_spots function on all entries. Entry construction is partially incomplete!
';
void_operation := 'true';
END IF;
my_limit_search_ac := '.';
ELSE
IF NOT EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewref')
THEN
IF NOT (SELECT make2db_reunit_refs(0))
THEN
RAISE NOTICE 'No result performing make2db_reunit_refs function. Entry construction is interrupted!
';
RETURN 'false';
END IF;
END IF;
IF NOT (SELECT make2db_reunit_spots(my_ac)) -- Construct ACs 1D and 2D Blocks in ViewSpotEntryLast -> general:("all")
THEN
RAISE NOTICE 'No result performing make2db_reunit_spots function for entry %. Entry construction is interrupted!
', my_ac;
RETURN 'false';
END IF;
my_limit_search_ac := my_ac;
END IF;
-- ...for each specified entry, we extract blocks using make2db_reunit_refs_ac(AC)
-- use SELECT make2db_reunit_refs("article_id") for a given article -> ViewRefLast
-- use PERFORM make2db_reunit_spots("accession_number") for a given Entry -> ViewSpotEntryLast
-- EXECUTE does not support SELECT yet, no way to use a (DYNAMIC) TEMPORARY TABLE with CREATE AS..!!
-- NON dynamic temporary tables are compiled ONCE and all reference to them fail in consequent calls.
SELECT INTO my_record databaseName FROM common.Database LIMIT 1;
IF (NOT FOUND) THEN
my_record.databaseName := 'the current database';
END IF;
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_make2db_construct_entry')
THEN
DELETE FROM buffer_make2db_construct_entry;
ELSE
CREATE TEMPORARY TABLE buffer_make2db_construct_entry (
identifier VARCHAR(32),
id_method VARCHAR(48),
accession_number VARCHAR(32),
secondary_identifiers TEXT,
creation TEXT,
version_2d TEXT,
version_general TEXT,
description TEXT,
genes TEXT,
organism TEXT,
organism_classification TEXT,
taxonomy_cross_reference TEXT,
masters TEXT,
images TEXT,
free_comments TEXT,
reference_lines TEXT,
one_d_comments TEXT,
one_d_blocks TEXT,
two_d_comments TEXT,
two_d_blocks TEXT,
database_cross_reference TEXT
);
END IF; -- Any change to buffer_make2d_construct_entry is to be reported in both upper and lower blocks
INSERT INTO buffer_make2db_construct_entry
SELECT Entry.ID AS identifier,
Entry.entryClass || '; ' || Entry.IdentMethod AS id_method,
Entry.AC AS accession_number, make2db_reunit_line(Entry.AC,'AC') AS secondary_identifiers,
creation.releaseDate || ', integrated into ' || my_record.databaseName || ' (release ' || creation.releaseNum || ')' AS creation,
EntryVersion2D.versionDate || ', 2D annotation version ' || EntryVersion2D.version AS version_2d,
EntryVersionGeneral.versionDate || ', general annotation version ' || EntryVersionGeneral.version AS version_general,
make2db_reunit_line(Entry.AC,'DE') AS description,
Entry.geneNames AS genes,
Organism.organismSpecies AS organism,
Organism.organismClassification AS organism_classification,
XrefDB.XrefDBName || '=' || Organism.taxonomyCode AS taxonomy_cross_reference,
make2db_reunit_line(Entry.AC,'MT') AS masters, -- Specific to Swiss2D-PAGE
make2db_reunit_line(Entry.AC,'IM') AS images,
make2db_reunit_line(Entry.AC,'CC') AS free_comments,
make2db_reunit_refs_ac(Entry.AC) AS reference_lines,
make2db_reunit_line(Entry.AC,'1C') AS one_d_comments,
make2db_reunit_line(Entry.AC,'1D') AS one_d_blocks,
make2db_reunit_line(Entry.AC,'2C') AS two_d_comments,
make2db_reunit_line(Entry.AC,'2D') AS two_d_blocks,
make2db_reunit_line(Entry.AC,'DR') AS database_cross_reference
FROM Entry, Release creation, EntryVersion2D, EntryVersionGeneral, XrefDB, Organism
WHERE Entry.releaseCreation = creation.releaseNum
AND Entry.AC = EntryVersion2D.AC
AND Entry.AC = EntryVersionGeneral.AC
AND Entry.organismID = Organism.organismID
AND Organism.taxonomyXrefDBCode = XrefDB.XrefDBCode
AND Entry.showFlagSwitch IS TRUE
/* to limit construction to the desired AC(s) */
AND Entry.AC ~* my_limit_search_ac
ORDER BY 3;
-- Entry.entryClass and Entry.IdentMethod could have been void
UPDATE buffer_make2db_construct_entry SET id_method = '' WHERE id_method = '; ';
IF NOT EXISTS (SELECT * FROM buffer_make2db_construct_entry LIMIT 1)
THEN
void_operation := 'true';
RAISE NOTICE 'No data was found to construct text view for entry/ies: %', my_ac;
ELSE
void_operation := 'false';
END IF;
/* We move the updated entries to the entries table in just one operation*/
PERFORM drop_class('T', 'tmp_buffer_entries','');
CREATE TABLE tmp_buffer_entries AS SELECT * FROM buffer_make2db_construct_entry;
COMMENT ON TABLE tmp_buffer_entries IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
GRANT SELECT ON tmp_buffer_entries TO select2d;
IF my_ac = 'all'
THEN
PERFORM drop_class('T', 'ViewEntry', ''); -- Indexes are automatically droped
ALTER TABLE tmp_buffer_entries RENAME TO ViewEntry;
CREATE INDEX ViewEntry_ac_idx ON ViewEntry(accession_number);
CREATE INDEX ViewEntry_id_idx ON ViewEntry(identifier);
RAISE NOTICE 'Full Entries Table has been constructed/updated!
';
ELSE
DELETE FROM ViewEntry WHERE accession_number::VARCHAR(32) = my_ac;
INSERT INTO ViewEntry (SELECT * FROM buffer_make2db_construct_entry);
PERFORM drop_class('T', 'tmp_last_entry', '');
ALTER TABLE tmp_buffer_entries RENAME TO tmp_last_entry;
END IF;
DELETE FROM buffer_make2db_construct_entry;
-- ANALYZE ViewEntry; -- KHM (server shuts down in mordor!!)
IF (void_operation) THEN
RETURN 'false';
ELSE
RETURN 'true';
END IF;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO EXPORT ASCII ENTRY(IES) IN STANDARD TEXT FORMAT.
Ouput will have litteral \n sequences, so the file should be parsed to convert those sequences into real \n characters
-- FUNCTION TO EXPORT ASCII ENTRY(IES) IN STANDARD TEXT FORMAT
--------------------------------------------------------------
-- Output will have litteral \n sequences, so the file should be parsed to convert thoses sequences into real \n characters
DECLARE
my_ac VARCHAR(32);
my_line_length INT;
my_hide_private TEXT;
my_file TEXT;
my_file_command TEXT;
my_record RECORD;
-- my_database_name TEXT;
BEGIN
my_file := '''' || $3 || '''';
my_line_length := $2;
IF my_line_length <25 THEN my_line_length = 75;
END IF;
my_ac := $1;
my_hide_private := $4;
-- CREATE TEMPORARY TABLE export_ascii_entries (make2db_ascii_entry TEXT); !! still no (select...into) with execute
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_export_ascii_entries')
THEN
DELETE FROM buffer_export_ascii_entries; -- No need to lock table (serializable level is set on)
ELSE
CREATE TEMPORARY TABLE buffer_export_ascii_entries (make2db_ascii_entry TEXT);
END IF;
IF my_ac = '' OR my_ac = 'all' THEN
FOR my_record IN SELECT AC FROM entry WHERE showFlagSwitch = 'true' ORDER BY ID
LOOP
INSERT INTO buffer_export_ascii_entries SELECT make2db_ascii_entry(my_record.AC, my_line_length, my_hide_private);
END LOOP;
ELSE
INSERT INTO buffer_export_ascii_entries SELECT make2db_ascii_entry(my_ac, my_line_length, my_hide_private);
END IF;
my_file_command := 'COPY buffer_export_ascii_entries TO ' || my_file;
EXECUTE my_file_command;
EXECUTE 'DELETE FROM buffer_export_ascii_entries';
RETURN 'true';
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO BUILD PROTEINS LIST FOR EACH MAP
-- FUNCTION TO BUILD PROTEINS LIST FOR EACH MAP
-----------------------------------------------
DECLARE
my_record RECORD;
my_record2 RECORD;
my_record3 RECORD;
my_record_maps_number RECORD;
my_record_maps_name RECORD;
my_array_length INT2;
my_description_string TEXT;
my_mapping_string TEXT;
my_results_string TEXT;
my_RN_string TEXT;
my_RF_string TEXT;
my_this_reference TEXT;
my_variable_string TEXT;
void_operation BOOLEAN;
BEGIN
void_operation := 'false';
RAISE NOTICE 'Protein list in progress...';
-- ANALYSE; -- KHM (server shuts down in mordor!!)
IF NOT EXISTS (SELECT AC FROM EntryGelImage LIMIT 1)
THEN
RAISE NOTICE 'No entries found to construct protein lists on maps. List will be empty!
';
void_operation := 'true';
END IF;
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_make2db_map_protein_list')
THEN
DELETE FROM buffer_make2db_map_protein_list; -- No need to lock table (serializable level is set on)
ELSE
CREATE TEMPORARY TABLE buffer_make2db_map_protein_list
( gelID INT4,
genes VARCHAR(1024),
description TEXT,
spotID VARCHAR(16),
AC VARCHAR(32),
ID VARCHAR(32),
pI NUMERIC(4,2),
mw NUMERIC(6,3),
volumeRelative FLOAT4,
odRelative FLOAT4,
fragment BOOLEAN,
topicDescription TEXT,
mappingTechniques TEXT,
availableResults TEXT,
RN_References TEXT,
referenceIDs TEXT,
showFlag BOOLEAN NOT NULL DEFAULT 'true',
showFlagSwitch BOOLEAN NOT NULL DEFAULT 'true'
CHECK ((showFlag IS TRUE AND showFlagSwitch IS TRUE) OR showFlag IS NOT TRUE)
);
END IF;
IF NOT (void_operation) THEN
RAISE NOTICE 'Protein Lists are being now processed for each Map. Please wait!...';
END IF;
INSERT INTO buffer_make2db_map_protein_list
SELECT DISTINCT SpotEntry.gelID, Entry.geneNames as genes, Entry.description, SpotEntry.spotID,
Entry.AC, Entry.ID as ID,
Spot.pI, (Spot.mw)/1000.0, Spot.volumeRelative, Spot.odRelative, SpotEntry.fragment
FROM SpotEntry JOIN (Entry JOIN EntryGelImage ON (Entry.AC = EntryGelImage.AC ))
ON (SpotEntry.AC = Entry.AC),
Spot
WHERE (Spot.spotID = SpotEntry.spotID AND Spot.gelID = SpotEntry.gelID
AND SpotEntry.showFlagSwitch IS TRUE
);
DELETE FROM buffer_make2db_map_protein_list
WHERE buffer_make2db_map_protein_list.gelID IN (SELECT gelID FROM Gel WHERE showFlagSwitch IS FALSE);
IF NOT (void_operation) THEN
RAISE NOTICE '... Protein lists for the different maps are still in progress...
';
END IF;
UPDATE buffer_make2db_map_protein_list SET genes = '-' WHERE genes IS NULL;
UPDATE buffer_make2db_map_protein_list SET showFlag = Entry.showFlag
FROM ENTRY
WHERE buffer_make2db_map_protein_list.AC = Entry.AC;
SELECT INTO my_record_maps_number max(gelID) AS max_number FROM Gel;
IF (my_record_maps_number.max_number IS NULL) AND NOT (void_operation) THEN
RAISE NOTICE 'No existing maps have been found to construct protein lists. Process in interrupted!
';
void_operation := 'true';
END IF;
-- Loop Over Each Map
IF (my_record_maps_number.max_number > 0) AND NOT (void_operation) THEN
FOR maps_ii IN 1..my_record_maps_number.max_number
LOOP
SELECT INTO my_record_maps_name shortName FROM Gel WHERE Gel.gelID = maps_ii AND Gel.showFlagSwitch IS TRUE;
IF my_record_maps_name.shortName IS NOT NULL THEN
RAISE NOTICE '... % is being processed', my_record_maps_name.shortName;
END IF;
FOR my_record IN
SELECT gelID, spotID, AC FROM buffer_make2db_map_protein_list WHERE gelID = maps_ii
LOOP -- For Every Line of the Selected Map
my_description_string := '';
my_mapping_string := '';
my_results_string := '';
my_RN_string := '';
my_RF_string := '';
IF ( EXISTS ( SELECT * FROM SpotEntryGeneralTopic WHERE spotID = my_record.spotID
AND gelID = my_record.gelID AND AC = my_record.AC LIMIT 1 )
OR EXISTS ( SELECT * FROM SpotEntryMappingTopic WHERE spotID = my_record.spotID
AND gelID = my_record.gelID AND AC = my_record.AC LIMIT 1 )
)
THEN
FOR my_record2 IN -- grouped General topic description, possibly over several lines
SELECT topicName, allReferences, ambiguousReference FROM GeneralTopicDefinition, GeneralTopicEntryData, SpotEntryGeneralTopic
WHERE SpotEntryGeneralTopic.spotID = my_record.spotID
AND SpotEntryGeneralTopic.gelID = my_record.gelID AND SpotEntryGeneralTopic.AC = my_record.AC
AND SpotEntryGeneralTopic.topicDataID = GeneralTopicEntryData.topicDataID
AND GeneralTopicEntryData.generalTopicID = GeneralTopicDefinition.generalTopicID
-- AND ambiguousReference = 'false'
ORDER BY GeneralTopicDefinition.topicName, GeneralTopicEntryData.topicDataText
-- UNION -> Does not work here, so we retype the entire querry for mapping methods
LOOP
IF my_description_string !~ my_record2.topicName
THEN
my_description_string := my_description_string || my_record2.topicName || ', ';
END IF;
FOR ii IN 1..99
LOOP
IF my_record2.allReferences[1] IS NULL AND (my_record2.ambiguousReference)
THEN
my_RN_string := '1, ';
SELECT INTO my_record3 referenceID FROM ReferencedEntry WHERE AC = my_record.AC AND RNdisplayedValue = 1 LIMIT 1;
my_RF_string := my_record3.referenceID::TEXT || ', ';
EXIT;
END IF;
IF my_record2.allReferences[ii] IS NULL THEN EXIT;
END IF;
my_this_reference := my_record2.allReferences[ii]::TEXT || ', ';
IF my_RN_string !~ my_this_reference
THEN
my_RN_string := my_RN_string || my_this_reference;
SELECT INTO my_record3 referenceID FROM ReferencedEntry
WHERE AC = my_record.AC AND RNdisplayedValue = my_record2.allReferences[ii] LIMIT 1;
my_RF_string := my_RF_string || my_record3.referenceID::TEXT || ', ';
END IF;
END LOOP;
END LOOP;
-- UNION -> Does not work here, we retype the entire querry for mapping methods
FOR my_record2 IN -- grouped General topic description, possibly over several lines
SELECT 'MAPPING'::VARCHAR(64) as topicName, allReferences,
ambiguousReference FROM GeneralTopicEntryData, SpotEntryMappingTopic
WHERE SpotEntryMappingTopic.spotID = my_record.spotID
AND SpotEntryMappingTopic.gelID = my_record.gelID AND SpotEntryMappingTopic.AC = my_record.AC
AND SpotEntryMappingTopic.topicDataID = GeneralTopicEntryData.topicDataID
-- AND ambiguousReference = 'false'
LOOP
IF my_description_string !~ my_record2.topicName
THEN
my_description_string := my_description_string || my_record2.topicName || ', ';
END IF;
FOR ii IN 1..99
LOOP
IF my_record2.allReferences[1] IS NULL AND (my_record2.ambiguousReference)
THEN
IF (my_RN_string ~ '^1,' OR my_RN_string ~ ' 1,') THEN EXIT; END IF;
my_RN_string := '1, ' || my_RN_string;
SELECT INTO my_record3 referenceID FROM ReferencedEntry WHERE AC = my_record.AC AND RNdisplayedValue = 1 LIMIT 1;
my_RF_string := my_RF_string || my_record3.referenceID::TEXT || ', ';
EXIT;
END IF;
IF my_record2.allReferences[ii] IS NULL THEN EXIT;
END IF;
my_this_reference := my_record2.allReferences[ii]::TEXT || ', ';
IF my_RN_string !~ my_this_reference
THEN
my_RN_string := my_RN_string || my_this_reference;
SELECT INTO my_record3 referenceID FROM ReferencedEntry
WHERE AC = my_record.AC AND RNdisplayedValue = my_record2.allReferences[ii] LIMIT 1;
my_RF_string := my_RF_string || my_record3.referenceID::TEXT || ', ';
END IF;
END LOOP;
END LOOP;
my_description_string := substr(my_description_string, 1, length(my_description_string)-2);
my_RN_string := substr(my_RN_string, 1, length(my_RN_string)-2);
my_RF_string := substr(my_RF_string, 1, length(my_RF_string)-2);
END IF;
-- Now, if no associated Topic has been found for that spot, we refer it to the first defined article (RN=1) KHM
IF my_RN_string is NULL or my_RN_string = ''
THEN
my_RN_string := '1';
SELECT INTO my_record3 referenceID FROM ReferencedEntry WHERE AC = my_record.AC AND RNdisplayedValue = my_RN_string LIMIT 1;
my_RF_string := my_RF_string || my_record3.referenceID::TEXT;
END IF;
-- Concatenate mapping methods
my_mapping_string := my_mapping_string ||
common.make2db_entryspot_mapping_methods_string(my_record.AC, my_record.spotID, my_record.gelID);
-- Any Experimental results of PMF, Aa or MS/MS (PeptSeq)?
my_results_string := '(';
my_variable_string := '';
IF (length(my_mapping_string) > 0) THEN
my_variable_string := ' ';
END IF;
IF EXISTS ( SELECT * FROM SpotIdentificationPeptMassF WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC AND showFlagSwitch = 'true' LIMIT 1)
THEN
my_results_string := my_results_string || 'PMF';
IF (my_mapping_string !~ '[{,]PMF[,}]') THEN
my_mapping_string := my_mapping_string || my_variable_string || '{PMF}';
my_variable_string := ' ';
END IF;
END IF;
IF EXISTS ( SELECT * FROM SpotIdentificationAAcid WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC AND showFlagSwitch = 'true' LIMIT 1)
THEN
IF length(my_results_string) > 2 THEN my_results_string := my_results_string || ',';
END IF;
my_results_string := my_results_string || 'Aa';
IF (my_mapping_string !~ '[{,]Aa[,}]') THEN
my_mapping_string := my_mapping_string || my_variable_string || '{Aa}';
my_variable_string := ' ';
END IF;
END IF;
IF EXISTS ( SELECT * FROM SpotIdentificationTandemMS WHERE spotID = my_record.spotID
AND gelID = my_record.gelID
AND AC = my_record.AC AND showFlagSwitch = 'true' LIMIT 1)
THEN
IF length(my_results_string) > 2 THEN my_results_string := my_results_string || ',';
END IF;
my_results_string := my_results_string || 'MS/MS';
IF (my_mapping_string !~ '[{,]MS/MS[,}]') THEN
my_mapping_string := my_mapping_string || my_variable_string || '{MS/MS}';
END IF;
END IF;
my_results_string := my_results_string || ')';
IF my_description_string = '' THEN my_description_string := '-';
END IF;
IF my_mapping_string = '' THEN my_mapping_string := '-';
END IF;
IF length(my_results_string) < 4 THEN my_results_string := '-';
END IF;
UPDATE buffer_make2db_map_protein_list
SET topicDescription = my_description_string, mappingTechniques = my_mapping_string,
availableResults = my_results_string, RN_References = my_RN_string, referenceIDs = my_RF_string
WHERE buffer_make2db_map_protein_list.spotID = my_record.spotID
AND buffer_make2db_map_protein_list.gelID = my_record.gelID
AND buffer_make2db_map_protein_list.AC = my_record.AC;
END LOOP; -- END LOOP For Every Line of the Selected Map
END LOOP;
END IF;
-- END Loop Over Each Map
IF NOT EXISTS ( SELECT * FROM buffer_make2db_map_protein_list LIMIT 1 ) THEN
void_operation := 'true';
RAISE NOTICE 'No data to construct the map protein lists.';
ELSE
void_operation := 'false';
END IF;
-- Move the buffer table to the permanent one:
-- EXECUTE statements do not support SELECT yet!! Till then, we adopt this locked *concurrential* solution
-->(eachs exectuion deletes the result of the previous one!!)
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewmapentrylist')
THEN
LOCK TABLE ViewMapEntryList IN ACCESS EXCLUSIVE MODE; -- Any concurrential transaction will wait for this one
DELETE FROM ViewMapEntryList;
INSERT INTO ViewMapEntryList SELECT * FROM buffer_make2db_map_protein_list ORDER by 1;
ELSE
CREATE TABLE ViewMapEntryList AS SELECT * FROM buffer_make2db_map_protein_list ORDER by 1;
CREATE INDEX ViewMapEntryList_gelID ON ViewMapEntryList (gelID);
CREATE INDEX ViewMapEntryList_spotID ON ViewMapEntryList (spotID);
CREATE INDEX ViewMapEntryList_AC_idx ON ViewMapEntryList (AC);
COMMENT ON TABLE ViewMapEntryList IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
GRANT SELECT ON ViewMapEntryList TO select2d;
END IF;
DELETE FROM buffer_make2db_map_protein_list;
-- ANALYZE ViewMapEntryList; -- KHM (server shuts down in mordor!!)
IF (void_operation) THEN
RETURN 'false';
ELSE
RETURN 'true';
END IF;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO REUNIFY GENERAL REFERENCE BLOCKS
(use make2db_reunit_refs(0) to reunify all articles, otherwise pass the article id)
-- FUNCTION TO REUNIFY GENERAL REFERENCE BLOCKS
-----------------------------------------------
-- use make2db_reunit_refs(0) to reunify all articles, otherwise pass the article id
DECLARE
my_article ALIAS for $1;
my_record RECORD;
my_record2 RECORD;
my_record3 RECORD;
my_max_author_group_priority INT2;
my_author_group_string VARCHAR(2048);
my_max_author_priority INT2;
my_author_string VARCHAR(8192);
my_rx_array TEXT;
ii INT2;
void_operation BOOLEAN;
BEGIN
void_operation := 'false';
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_make2db_reunit_refs') -- for postgres 7.3+ use schema (buffer.)
THEN
DELETE FROM buffer_make2db_reunit_refs; -- No need to lock table (serializable level is set on)
ELSE
CREATE TEMPORARY TABLE buffer_make2db_reunit_refs
( referenceID INT4 UNIQUE, referenceWorkDescription VARCHAR(64),
crossReferences VARCHAR(256), authorsGroup VARCHAR(2048), authors VARCHAR(8192), referenceTitle TEXT, referenceLocation TEXT
);
END IF;
IF my_article = 0
THEN
INSERT INTO buffer_make2db_reunit_refs (referenceID) SELECT referenceID FROM Reference ORDER BY 1;
ELSE
INSERT INTO buffer_make2db_reunit_refs (referenceID) SELECT referenceID FROM Reference WHERE Reference.referenceID = my_article;
END IF;
FOR my_record IN
SELECT referenceID FROM buffer_make2db_reunit_refs ORDER BY 1
LOOP
UPDATE buffer_make2db_reunit_refs SET referenceWorkDescription = ReferenceWork.referenceWorkDescription || '.'
FROM Reference, ReferenceWork
WHERE Reference.referenceID = my_record.referenceID AND ReferenceWork.referenceWorkID = Reference.referenceWorkID
AND buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
IF EXISTS (SELECT referenceID FROM ReferenceLocationJournal WHERE referenceID = my_record.referenceID)
THEN
my_rx_array := '';
SELECT INTO my_record2 ReferenceLocationJournal.crossReferences FROM ReferenceLocationJournal WHERE ReferenceLocationJournal.referenceID = my_record.referenceID;
-- Since postgreSQL 7.4: use Numerical array_upper and array_lower rather than array_dims
SELECT INTO my_record3 array_upper(ReferenceLocationJournal.crossReferences, 1) AS rx_upper FROM ReferenceLocationJournal
WHERE ReferenceLocationJournal.referenceID = my_record.referenceID;
FOR ii IN 1..my_record3.rx_upper -- for postgres 7.4 and higher
-- FOR ii IN 1..5
LOOP
IF my_record2.crossReferences[ii][2] IS NOT NULL and my_record2.crossReferences[ii][2] <> '0' THEN
my_rx_array := my_rx_array || my_record2.crossReferences[ii][1] || '=' || my_record2.crossReferences[ii][2] || '; ';
END IF;
END LOOP;
IF (length(my_rx_array) > 0) THEN
my_rx_array = substr(my_rx_array, 0, length(my_rx_array));
END IF;
UPDATE buffer_make2db_reunit_refs SET crossReferences = my_rx_array WHERE buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
END IF;
my_max_author_group_priority := max(authorPriority) FROM ONLY AuthorGroup WHERE article = my_record.referenceID;
my_author_group_string := '';
IF my_max_author_group_priority > 0 THEN
FOR ii IN 1..my_max_author_group_priority
LOOP
FOR my_record2 IN
SELECT author FROM ONLY AuthorGroup WHERE AuthorGroup.article = my_record.referenceID AND AuthorGroup.authorPriority = ii
LOOP
my_author_group_string := my_author_group_string || my_record2.author || ' & ';
END LOOP;
END LOOP;
IF my_author_group_string <> '' THEN
my_author_group_string = substr(my_author_group_string, 0, length(my_author_group_string)-2) || ';';
END IF;
UPDATE buffer_make2db_reunit_refs SET authorsGroup = my_author_group_string WHERE buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
END IF;
my_max_author_priority := max(authorPriority) FROM ONLY Author WHERE article = my_record.referenceID;
my_author_string := '';
FOR ii IN 1..my_max_author_priority
LOOP
FOR my_record2 IN
SELECT author FROM ONLY Author WHERE Author.article = my_record.referenceID AND Author.authorPriority = ii
LOOP
my_author_string := my_author_string || my_record2.author || ', ';
END LOOP;
END LOOP;
my_author_string = substr(my_author_string, 0, length(my_author_string)-1) || ';';
UPDATE buffer_make2db_reunit_refs SET authors = my_author_string WHERE buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
UPDATE buffer_make2db_reunit_refs SET referenceTitle = '''''' || Reference.referenceTitle || ''''';'
FROM Reference
WHERE Reference.referenceID = my_record.referenceID AND buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
UPDATE buffer_make2db_reunit_refs SET referenceLocation = make2db_rl_reconstruct(my_record.referenceID,'')
WHERE buffer_make2db_reunit_refs.referenceID = my_record.referenceID;
END LOOP;
IF NOT EXISTS (SELECT * FROM buffer_make2db_reunit_refs LIMIT 1) THEN
void_operation := 'true';
RAISE NOTICE 'No references found to fill in ViewRef.';
ELSE
void_operation := 'false';
END IF;
-- Move the buffer table to the permanent one:
-- EXECUTE statements do not support SELECT yet!! Till then, we adopt this locked *concurrential* solution
-->(eachs exectuion deletes the result of the previous one!!)
IF my_article = 0
THEN
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewref')
THEN
LOCK TABLE ViewRef IN ACCESS EXCLUSIVE MODE; -- Any concurrential transaction will wait for this one
DELETE FROM ViewRef;
INSERT INTO ViewRef SELECT * FROM buffer_make2db_reunit_refs ORDER by 1;
ELSE
CREATE TABLE ViewRef AS SELECT * FROM buffer_make2db_reunit_refs ORDER by 1;
CREATE INDEX ViewRef_referenceID_idx ON ViewRef(referenceID);
COMMENT ON TABLE ViewRef IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
GRANT SELECT ON ViewRef TO select2d;
END IF;
-- ANALYZE ViewRef; -- KHM (server shuts down in mordor!!)
ELSE
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewreflast')
THEN
LOCK TABLE ViewRefLast IN ACCESS EXCLUSIVE MODE;
DELETE FROM ViewRefLast;
INSERT INTO ViewRefLast SELECT * FROM buffer_make2db_reunit_refs;
ELSE
CREATE TABLE ViewRefLast AS SELECT * FROM buffer_make2db_reunit_refs;
COMMENT ON TABLE ViewRefLast IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
GRANT SELECT ON ViewRefLast TO select2d;
END IF;
END IF;
DELETE FROM buffer_make2db_reunit_refs;
IF (void_operation) THEN
RETURN 'false';
ELSE
RETURN 'true';
END IF;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO REUNIFY REFERENCE BLOCKS FOR A GIVEN ENTRY
-- FUNCTION TO REUNIFY REFERENCE BLOCKS FOR A GIVEN ENTRY
---------------------------------------------------------
DECLARE
my_ac ALIAS for $1;
my_record RECORD;
my_record2 RECORD;
my_ref_blocks TEXT;
ii INT2;
BEGIN
my_ref_blocks = '';
FOR my_record IN
SELECT ReferencedEntry.referenceID, ReferencedEntry.RNdisplayedValue FROM ReferencedEntry WHERE ReferencedEntry.AC::VARCHAR(32) = my_ac ORDER BY 2
LOOP
SELECT INTO my_record2 referenceWorkDescription, crossReferences, authorsGroup, authors, referenceTitle, referenceLocation FROM ViewRef
WHERE referenceID = my_record.referenceID;
IF my_ref_blocks <> '' THEN
my_ref_blocks := my_ref_blocks || '
';
END IF;
my_ref_blocks := my_ref_blocks || 'RN [' || my_record.RNdisplayedValue || ']
RP ' || my_record2.referenceWorkDescription;
IF my_record2.crossReferences <> '' THEN
my_ref_blocks := my_ref_blocks || '
RX ' || my_record2.crossReferences;
END IF;
IF my_record2.authorsGroup <> '' THEN
my_ref_blocks := my_ref_blocks || '
RG ' || my_record2.authorsGroup;
END IF;
my_ref_blocks := my_ref_blocks || '
RA ' || my_record2.authors;
IF my_record2.referenceTitle <> '' THEN
my_ref_blocks := my_ref_blocks || '
RT ' || my_record2.referenceTitle;
END IF;
my_ref_blocks := my_ref_blocks || '
RL ' || my_record2.referenceLocation;
UPDATE ViewRef SET referenceWorkDescription = ReferenceWork.referenceWorkDescription || '.'
FROM Reference, ReferenceWork
WHERE Reference.referenceID = my_record.referenceID AND ReferenceWork.referenceWorkID = Reference.referenceWorkID
AND ViewRef.referenceID = my_record.referenceID;
END LOOP;
RETURN my_ref_blocks;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO REUNIFY ENTRIES 1/2D BLOCKS
-- FUNCTION TO REUNIFY ENTRIES 1/2D BLOCKS
------------------------------------------
DECLARE
my_ac ALIAS for $1;
my_record RECORD;
my_record2 RECORD;
my_record3 RECORD;
my_max_version INT4;
my_amino_acids TEXT;
my_msms TEXT;
my_parentIon_mass FLOAT;
my_parentIon_charge INT2;
my_chargeSign VARCHAR(32);
my_parentIon_text TEXT;
my_peptide_sequences TEXT;
my_peptide_sequences_subset TEXT;
my_peptide_masses TEXT;
my_array_upper_dim INT4;
my_enzyme TEXT;
my_last_data_doc TEXT;
my_last_data_doc_uri TEXT;
my_last_identification_doc TEXT;
my_last_identification_doc_uri TEXT;
my_show_flag BOOLEAN;
void_operation BOOLEAN;
BEGIN
void_operation := 'false';
my_show_flag := 'true';
IF my_ac = '' THEN RETURN 'false';
END IF;
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'buffer_make2db_reunit_spots')
THEN
DELETE FROM buffer_make2db_reunit_spots; -- No need to lock table (serializable level is set on)
ELSE
CREATE TEMPORARY TABLE buffer_make2db_reunit_spots
( spotID VARCHAR(16), gelID INT4, AC VARCHAR(32),
fragment BOOLEAN,
-- Specific data sets are separated by a line feed / version is the maximum version
AminoAcidList TEXT DEFAULT NULL,
aa_version INT4 DEFAULT NULL,
msms TEXT DEFAULT NULL,
ms_version INT4 DEFAULT NULL,
peptideSequences TEXT DEFAULT NULL,
peptseq_version INT4 DEFAULT NULL,
--peptideMasses FLOAT[][] DEFAULT NULL,
--enzyme VARCHAR(32) DEFAULT NULL,
peptideMasses TEXT DEFAULT NULL,
pmf_version INT4 DEFAULT NULL,
showFlag BOOLEAN NOT NULL DEFAULT 'true',
showFlagSwitch BOOLEAN NOT NULL DEFAULT 'true'
CHECK ((showFlag IS TRUE AND showFlagSwitch IS TRUE) OR showFlag IS NOT TRUE),
UNIQUE (spotID, gelID, AC)
);
END IF;
IF my_ac = 'all'
THEN
INSERT INTO buffer_make2db_reunit_spots (spotID, gelID, AC, fragment, showFlag) SELECT spotID, gelID, AC, fragment, showFlag
FROM SpotEntry WHERE SpotEntry.showFlagSwitch IS TRUE ORDER BY 1;
ELSE
INSERT INTO buffer_make2db_reunit_spots (spotID, gelID, AC, fragment, showFlag) SELECT spotID, gelID, AC, fragment, showFlag
FROM SpotEntry WHERE SpotEntry.AC::VARCHAR(32) = my_ac AND SpotEntry.showFlagSwitch IS TRUE ORDER BY 1;
END IF;
FOR my_record IN
SELECT spotID, gelID, AC FROM buffer_make2db_reunit_spots ORDER BY 1
LOOP
-- Amino Acid Composition part --
-- should we allow to add more than one record, or just one from the last annotated entry version? --
my_max_version := max(version) FROM SpotIdentificationAAcid WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC;
IF my_max_version IS NOT NULL
THEN
my_amino_acids = '';
FOR my_record2 IN
SELECT SpotIdentificationAAcid.AminoAcidList, SpotIdentificationAAcid.showFlag
FROM SpotIdentificationAAcid
WHERE SpotIdentificationAAcid.spotID = my_record.spotID AND SpotIdentificationAAcid.gelID = my_record.gelID
AND SpotIdentificationAAcid.AC = my_record.AC
-- AND SpotIdentificationAAcid.version = my_max_version
ORDER BY SpotIdentificationAAcid.version DESC
LOOP
my_amino_acids := my_amino_acids || my_record2.AminoAcidList ;
IF (my_record2.showFlag IS FALSE AND length(my_amino_acids) > 0) THEN
my_amino_acids := my_amino_acids || ' {private}';
END IF;
my_amino_acids := my_amino_acids || '
';
END LOOP;
IF (length(my_amino_acids) > 0) THEN -- erase the last
my_amino_acids := substr(my_amino_acids, 0, length(my_amino_acids));
END IF;
UPDATE buffer_make2db_reunit_spots SET AminoAcidList = my_amino_acids, aa_version = my_max_version
WHERE buffer_make2db_reunit_spots.spotID = my_record.spotID AND buffer_make2db_reunit_spots.gelID = my_record.gelID
AND buffer_make2db_reunit_spots.AC = my_record.AC;
END IF;
-- Mass Spectrometry part (Tandem MS) --
-- should we allow to add more than one record of the last annotated entry version? --
-- no direct relation is established between the subsets (peptides sequences) and the MS data for this view
my_max_version := max(version) FROM SpotIdentificationTandemMS WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC;
IF my_max_version IS NOT NULL
THEN
my_msms := '';
my_last_data_doc := '';
my_last_data_doc_uri := '';
my_last_identification_doc := '';
my_last_identification_doc_uri := '';
FOR my_record2 IN
SELECT SpotIdentificationTandemMS.ionMasses, SpotIdentificationTandemMS.dataExpID,
SpotIdentificationTandemMS.showFlag, SpotIdentificationTandemMS.allExperimentData,
SpotIdentificationTandemMS.identificationDocument, SpotIdentificationTandemMS.URI
FROM SpotIdentificationTandemMS
WHERE SpotIdentificationTandemMS.spotID = my_record.spotID AND SpotIdentificationTandemMS.gelID = my_record.gelID
AND SpotIdentificationTandemMS.AC = my_record.AC AND SpotIdentificationTandemMS.ionMasses IS NOT NULL
-- AND SpotIdentificationTandemMS.version = my_max_version
ORDER BY SpotIdentificationTandemMS.version, SpotIdentificationTandemMS.identificationDocument,
SpotIdentificationTandemMS.URI DESC
LOOP
my_parentIon_mass := 0.0;
my_parentIon_charge := 0;
SELECT INTO my_record3 parentMass, parentCharge, ionMasses, URI, dataDocument FROM SpotDataTandemMS
WHERE SpotDataTandemMS.dataExpID = my_record2.dataExpID
AND SpotDataTandemMS.spotID = my_record.spotID
AND SpotDataTandemMS.gelID = my_record.gelID
LIMIT 1;
my_array_upper_dim = array_upper(my_record2.ionMasses,1);
IF ( (my_record3.URI <> my_last_data_doc_uri OR my_record3.dataDocument <> my_last_data_doc OR
my_record2.URI <> my_last_identification_doc_uri OR my_record2.identificationDocument <> my_last_identification_doc)
AND
(my_record3.URI IS NOT NULL OR my_record3.dataDocument IS NOT NULL OR my_record2.URI IS NOT NULL OR my_record2.identificationDocument IS NOT NULL)
) THEN
my_msms := my_msms || ' [Documents] ';
IF (my_record3.URI IS NOT NULL) THEN
my_msms := my_msms || ' Data Document URI: ' || my_record3.URI;
my_last_data_doc_uri := my_record3.URI;
END IF;
IF (my_record3.dataDocument IS NOT NULL) THEN
my_msms := my_msms || ' Local Data Document: ' || my_record3.dataDocument;
my_last_data_doc := my_record3.dataDocument;
END IF;
IF (my_record2.URI IS NOT NULL) THEN
my_msms := my_msms || ' Identification Document URI: ' || my_record2.URI;
my_last_identification_doc_uri := my_record2.URI;
END IF;
IF (my_record2.identificationDocument IS NOT NULL) THEN
my_msms := my_msms || ' Local Identification Document: ' || my_record2.identificationDocument;
my_last_identification_doc := my_record2.identificationDocument;
END IF;
my_msms := my_msms || '
';
END IF;
IF (my_array_upper_dim > 0) THEN
IF (my_record3.parentCharge IS NOT NULL) OR (my_record3.parentMass > 0) THEN
my_parentIon_text := '';
IF (my_record3.parentMass > 0) THEN
my_parentIon_text := my_record3.parentMass::TEXT;
END IF;
IF (my_record3.parentCharge IS NOT NULL) THEN
IF (length(my_parentIon_text) > 0) THEN my_parentIon_text := my_parentIon_text || ':'; END IF;
my_chargeSign = ' -> charge not reported';
IF (my_record3.parentCharge >0) THEN my_chargeSign = '+';
ELSE IF (my_record3.parentCharge <0) THEN my_chargeSign = '-';
END IF; END IF;
my_parentIon_charge = abs(my_record3.parentCharge)::TEXT;
my_parentIon_text := my_parentIon_text || my_parentIon_charge || my_chargeSign;
END IF;
my_msms := my_msms || '[' || my_parentIon_text || '] ';
END IF;
FOR ii in 1..my_array_upper_dim
LOOP
-- we skip zero values (0.0 by convention is for undefined data)
IF (my_record2.ionMasses[ii][1] > 0 OR my_record2.ionMasses[ii][2] > 0) THEN
my_msms := my_msms || my_record2.ionMasses[ii][1];
IF (my_record2.ionMasses[ii][2] > 0) THEN
my_msms := my_msms || ' (' || my_record2.ionMasses[ii][2] || ')';
END IF;
my_msms := my_msms || '; ';
END IF;
END LOOP;
my_array_upper_dim = array_upper(my_record3.ionMasses,1);
IF (my_record2.allExperimentData IS FALSE AND my_array_upper_dim > 0) THEN
my_msms := my_msms || ' All Experiment Data: ';
FOR ii in 1..my_array_upper_dim
LOOP
my_msms := my_msms || my_record3.ionMasses[ii][1];
IF (my_record3.ionMasses[ii][2] > 0) THEN
my_msms := my_msms || ' (' || my_record3.ionMasses[ii][2] || ')';
END IF;
my_msms := my_msms || '; ';
END LOOP;
END IF;
END IF;
IF (my_record2.showFlag IS FALSE AND length(my_msms) > 0) THEN
my_msms := my_msms || ' {private}';
END IF;
IF (length(my_msms) < 3) THEN my_msms:= '--'; END IF;
my_msms := my_msms || '
';
END LOOP;
IF (length(my_msms) > 0) THEN -- erase the last
my_msms := substr(my_msms, 0, length(my_msms));
ELSE
my_msms = NULL;
END IF;
UPDATE buffer_make2db_reunit_spots SET msms = my_msms, ms_version = my_max_version
WHERE buffer_make2db_reunit_spots.spotID = my_record.spotID AND buffer_make2db_reunit_spots.gelID = my_record.gelID
AND buffer_make2db_reunit_spots.AC = my_record.AC;
my_msms := '';
END IF;
-- Peptide Sequences (sub-set of Tandem MS) --
-- should we allow to add more than one record from the last annotated entry version? --
my_max_version := max(version) FROM SpotIdentificationTandemMS WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC AND SpotIdentificationTandemMS.hasSubset IS TRUE;
IF my_max_version IS NOT NULL -- identifiedPeptideSequence
THEN
my_peptide_sequences := '';
FOR my_record2 IN
SELECT SpotIdentificationTandemMS.identificationID, SpotIdentificationTandemMS.showFlag
FROM SpotIdentificationTandemMS
WHERE SpotIdentificationTandemMS.spotID = my_record.spotID AND SpotIdentificationTandemMS.gelID = my_record.gelID
AND SpotIdentificationTandemMS.AC = my_record.AC AND SpotIdentificationTandemMS.hasSubset IS TRUE
-- AND SpotIdentificationTandemMS.version = my_max_version
ORDER BY SpotIdentificationTandemMS.version DESC
LOOP
my_peptide_sequences_subset := '';
FOR my_record3 IN
SELECT SpotIdentificationTandemMSSubset.identifiedPeptideSequence, SpotIdentificationTandemMSSubset.sequenceStartPosition,
SpotIdentificationTandemMSSubset.sequenceENDPosition
FROM SpotIdentificationTandemMSSubset
WHERE SpotIdentificationTandemMSSubset.identificationID = my_record2.identificationID
ORDER BY 2,3,1
LOOP
my_peptide_sequences_subset := my_peptide_sequences_subset || my_record3.identifiedPeptideSequence;
IF (my_record3.sequenceStartPosition > 0 AND my_record3.sequenceEndPosition > 0)
THEN
my_peptide_sequences_subset := my_peptide_sequences_subset || ',' ||
CAST(my_record3.sequenceStartPosition AS TEXT) || '-' || CAST(my_record3.sequenceENDPosition AS TEXT);
END IF;
my_peptide_sequences_subset := my_peptide_sequences_subset || '; ';
END LOOP;
IF (length(my_peptide_sequences_subset) > 0) THEN
my_peptide_sequences_subset := substr(my_peptide_sequences_subset, 0, length(my_peptide_sequences_subset)-1);
IF my_record2.showFlag IS FALSE THEN
my_peptide_sequences_subset := my_peptide_sequences_subset || ' {private}';
END IF;
my_peptide_sequences := my_peptide_sequences || my_peptide_sequences_subset || '
';
END IF;
END LOOP;
IF (length(my_peptide_sequences) > 0) THEN -- erase the last
my_peptide_sequences := substr(my_peptide_sequences, 0, length(my_peptide_sequences));
END IF;
UPDATE buffer_make2db_reunit_spots SET peptideSequences = my_peptide_sequences, peptseq_version = my_max_version
WHERE buffer_make2db_reunit_spots.spotID = my_record.spotID AND buffer_make2db_reunit_spots.gelID = my_record.gelID
AND buffer_make2db_reunit_spots.AC = my_record.AC;
END IF;
-- Peptide Masses part --
-- should we allow to add more than one record of the last annotated entry version? --
my_max_version := max(version) FROM SpotIdentificationPeptMassF WHERE spotID = my_record.spotID AND gelID = my_record.gelID
AND AC = my_record.AC;
IF my_max_version IS NOT NULL
THEN
my_peptide_masses := '';
my_msms := '';
my_last_data_doc := '';
my_last_data_doc_uri := '';
my_last_identification_doc := '';
my_last_identification_doc_uri := '';
FOR my_record2 IN
SELECT SpotIdentificationPeptMassF.peptideMasses, SpotIdentificationPeptMassF.dataExpID,
SpotIdentificationPeptMassF.showFlag, SpotIdentificationPeptMassF.allExperimentData,
SpotIdentificationPeptMassF.identificationDocument, SpotIdentificationPeptMassF.URI
FROM SpotIdentificationPeptMassF
WHERE SpotIdentificationPeptMassF.spotID = my_record.spotID AND SpotIdentificationPeptMassF.gelID = my_record.gelID
AND SpotIdentificationPeptMassF.AC = my_record.AC
-- AND SpotIdentificationPeptMassF.version = my_max_version
ORDER BY SpotIdentificationPeptMassF.version, SpotIdentificationPeptMassF.identificationDocument,
SpotIdentificationPeptMassF.URI DESC
LOOP
my_enzyme := '';
SELECT INTO my_record3 enzyme, peptideMasses, URI, dataDocument FROM SpotDataPeptMassF
WHERE SpotDataPeptMassF.dataExpID = my_record2.dataExpID
AND SpotDataPeptMassF.spotID = my_record.spotID
AND SpotDataPeptMassF.gelID = my_record.gelID
LIMIT 1;
IF (length(my_record3.enzyme ) > 0) THEN
my_enzyme := my_record3.enzyme;
ELSE
my_enzyme := '(Undefined Enzyme)';
END IF;
my_array_upper_dim = array_upper(my_record2.peptideMasses,1);
IF ( (my_record3.URI <> my_last_data_doc_uri OR my_record3.dataDocument <> my_last_data_doc OR
my_record2.URI <> my_last_identification_doc_uri OR my_record2.identificationDocument <> my_last_identification_doc)
AND
(my_record3.URI IS NOT NULL OR my_record3.dataDocument IS NOT NULL OR my_record2.URI IS NOT NULL OR my_record2.identificationDocument IS NOT NULL)
) THEN
my_peptide_masses := my_peptide_masses || ' [Documents] ';
IF (my_record3.URI IS NOT NULL) THEN
my_peptide_masses := my_peptide_masses || ' Data Document URI: ' || my_record3.URI;
my_last_data_doc_uri := my_record3.URI;
END IF;
IF (my_record3.dataDocument IS NOT NULL) THEN
my_peptide_masses := my_peptide_masses || ' Local Data Document: ' || my_record3.dataDocument;
my_last_data_doc := my_record3.dataDocument;
END IF;
IF (my_record2.URI IS NOT NULL) THEN
my_peptide_masses := my_peptide_masses || ' Identification Document URI: ' || my_record2.URI;
my_last_identification_doc_uri := my_record2.URI;
END IF;
IF (my_record2.identificationDocument IS NOT NULL) THEN
my_peptide_masses := my_peptide_masses || ' Local Identification Document: ' || my_record2.identificationDocument;
my_last_identification_doc := my_record2.identificationDocument;
END IF;
my_peptide_masses := my_peptide_masses || '
';
END IF;
IF (my_array_upper_dim > 0) THEN
FOR ii in 1..my_array_upper_dim
LOOP
-- we skip zero values (0.0 by convention is for undefined data)
IF (my_record2.peptideMasses[ii][1] > 0 OR my_record2.peptideMasses[ii][2] > 0) THEN
my_peptide_masses := my_peptide_masses || my_record2.peptideMasses[ii][1];
END IF;
IF (my_record2.peptideMasses[ii][2] > 0) THEN
my_peptide_masses := my_peptide_masses || ' (' || my_record2.peptideMasses[ii][2] || ')';
END IF;
my_peptide_masses := my_peptide_masses || '; ';
END LOOP;
my_array_upper_dim = array_upper(my_record3.peptideMasses,1);
IF (my_record2.allExperimentData IS FALSE AND my_array_upper_dim > 0) THEN
my_peptide_masses := my_peptide_masses || ' All Experiment Data: ';
FOR ii in 1..my_array_upper_dim
LOOP
my_peptide_masses := my_peptide_masses || my_record3.peptideMasses[ii][1];
IF (my_record3.peptideMasses[ii][2] > 0) THEN
my_peptide_masses := my_peptide_masses || ' (' || my_record3.peptideMasses[ii][2] || ')';
END IF;
my_peptide_masses := my_peptide_masses || '; ';
END LOOP;
END IF;
IF (length(my_peptide_masses) > 2) THEN
my_peptide_masses := my_peptide_masses || my_record3.enzyme;
END IF;
END IF;
IF (my_record2.showFlag IS FALSE AND length(my_peptide_masses) > 0) THEN
my_peptide_masses := my_peptide_masses || ' {private}';
END IF;
IF (length(my_peptide_masses) < 3) THEN my_peptide_masses := '--'; END IF;
my_peptide_masses := my_peptide_masses || '
';
END LOOP;
IF (length(my_peptide_masses) > 0) THEN -- erase the last
my_peptide_masses := substr(my_peptide_masses, 0, length(my_peptide_masses));
END IF;
UPDATE buffer_make2db_reunit_spots SET peptideMasses = my_peptide_masses, pmf_version = my_max_version
WHERE buffer_make2db_reunit_spots.spotID = my_record.spotID AND buffer_make2db_reunit_spots.gelID = my_record.gelID
AND buffer_make2db_reunit_spots.AC = my_record.AC;
END IF;
END LOOP;
IF NOT EXISTS (SELECT * FROM buffer_make2db_reunit_spots LIMIT 1) THEN
void_operation := 'true';
RAISE NOTICE 'No spots data to fill in ViewSpotEntry.';
ELSE
void_operation := 'false';
END IF;
-- Move the buffer table to the permanent one:
-- EXECUTE statements do not support SELECT yet!! Till then, we adopt this locked *concurrential* solution
-->(each exectuion deletes the result of the previous one!!)
IF my_ac = 'all'
THEN
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewspotentry')
THEN
LOCK TABLE ViewSpotEntry IN ACCESS EXCLUSIVE MODE; -- Any concurrential transaction will wait for this one
DELETE FROM ViewSpotEntry;
INSERT INTO ViewSpotEntry SELECT * FROM buffer_make2db_reunit_spots ORDER by 1;
ELSE
CREATE TABLE ViewSpotEntry AS SELECT * FROM buffer_make2db_reunit_spots ORDER by 1;
CREATE INDEX ViewSpotEntry_spotID_idx ON ViewSpotEntry(spotID);
CREATE INDEX ViewSpotEntry_gelID_idx ON ViewSpotEntry(gelID);
CREATE INDEX ViewSpotEntry_ac_idx ON ViewSpotEntry(AC);
COMMENT ON TABLE ViewSpotEntry IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
COMMENT ON COLUMN ViewSpotEntry.AminoAcidList IS 'Specific data sets are separated by
';
COMMENT ON COLUMN ViewSpotEntry.msms IS 'Specific data sets are separated by
';
COMMENT ON COLUMN ViewSpotEntry.peptideSequences IS 'Specific data sets are separated by
';
COMMENT ON COLUMN ViewSpotEntry.peptideMasses IS 'Specific data sets are separated by
';
GRANT SELECT ON ViewSpotEntry TO select2d;
END IF;
-- ANALYZE ViewSpotEntry; -- KHM (server shuts down in mordor!!)
ELSE
IF EXISTS (SELECT tablename FROM pg_tables WHERE lower(tablename) = 'viewspotentrylast')
THEN
LOCK TABLE ViewSpotEntryLast IN ACCESS EXCLUSIVE MODE;
DELETE FROM ViewSpotEntryLast;
INSERT INTO ViewSpotEntryLast SELECT * FROM buffer_make2db_reunit_spots;
ELSE
CREATE TABLE ViewSpotEntryLast AS SELECT * FROM buffer_make2db_reunit_spots;
COMMENT ON TABLE ViewSpotEntryLast IS
'THIS IS A VIEW-LIKE GENERATED TABLE INTENDED TO REPRESENT SOME DATA VIEWS! (NOT TO BE DIRECTLY EDITED)';
GRANT SELECT ON ViewSpotEntryLast TO select2d;
END IF;
DELETE FROM ViewSpotEntry WHERE ac::VARCHAR(32) = my_ac;
INSERT INTO ViewSpotEntry (SELECT * FROM buffer_make2db_reunit_spots);
END IF;
DELETE FROM buffer_make2db_reunit_spots;
IF (void_operation) THEN
RETURN 'false';
ELSE
RETURN 'true';
END IF;
END;
Returns: text
Language: PLPGSQL
FUNCTION TO CONSTRUCT THE REFERENCE LOCATION (RL LINE)
-- FUNCTION TO CONSTRUCT THE REFERENCE LOCATION (RL LINE)
---------------------------------------------------------
DECLARE
rl_id ALIAS for $1;
table_type_input ALIAS for $2;
table_type VARCHAR(32);
my_record RECORD;
my_record2 RECORD;
my_rl_line TEXT;
my_max_citer_priority INT2;
my_citer_string VARCHAR(800);
my_day INT2;
my_month INT2;
my_month_letter TEXT;
my_year INT2;
BEGIN
SET DATESTYLE TO 'POSTGRES, EUROPEAN';
table_type := table_type_input;
/* if table_type is not given */
IF table_type = ''
THEN
IF EXISTS (SELECT referenceID FROM ReferenceLocationJournal WHERE referenceID = rl_id AND unpublished = 'false')
THEN table_type := 'Journal';
ELSE IF EXISTS (SELECT referenceID FROM ReferenceLocationJournal WHERE referenceID = rl_id AND unpublished = 'true')
THEN table_type := 'Unpublished_results';
ELSE IF EXISTS (SELECT referenceID FROM ReferenceLocationBook WHERE referenceID = rl_id)
THEN table_type := 'Book';
ELSE IF EXISTS (SELECT referenceID FROM ReferenceLocationUnpubObservations
WHERE referenceID = rl_id)
THEN table_type := 'Unpublished observations';
ELSE IF EXISTS (SELECT referenceLocationThesis.referenceID FROM referenceLocationThesis WHERE referenceID = rl_id)
THEN table_type := 'Thesis';
ELSE IF EXISTS (SELECT referenceID FROM referenceLocationPatent WHERE referenceID = rl_id)
THEN table_type := 'Patent application';
ELSE IF EXISTS (SELECT referenceID FROM referenceLocationSubmission WHERE referenceID = rl_id)
THEN table_type := 'Submission';
ELSE IF EXISTS (SELECT referenceID FROM referenceLocationOther WHERE referenceID = rl_id)
THEN table_type := 'OTHER';
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
/* Category is Journal / Unpublished results */
IF table_type = 'Journal' OR table_type = 'Unpublished results'
THEN
SELECT INTO my_record Journal.journalName, Journal.url,
ReferenceLocationJournal.volume, ReferenceLocationJournal.subVolume, ReferenceLocationJournal.pageFirst, ReferenceLocationJournal.pageLast,
ReferenceLocationJournal.year, ReferenceLocationJournal.unpublished
FROM ReferenceLocationJournal, Journal
WHERE ReferenceLocationJournal.referenceID = rl_id AND Journal.journalID = ReferenceLocationJournal.journalID;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN rl_journal', rl_id;
RETURN '!ERROR: NO REF. % in the journal / unpublished results table!';
END IF;
my_rl_line := my_record.journalName || ' ' || my_record.volume;
IF my_record.subVolume IS NOT NULL
THEN
my_rl_line := my_rl_line || '(' || my_record.subVolume || ')';
END IF;
my_rl_line := my_rl_line || ':' || my_record.pageFirst || '-'
|| my_record.pageLast || '(' || my_record.year || ').';
IF my_record.unpublished = 'true' THEN
my_max_citer_priority = max(authorPriority) FROM Citer WHERE article = rl_id;
my_citer_string := '';
FOR ii IN 1..my_max_citerPriority
LOOP
FOR my_record2 IN
SELECT author FROM Citer WHERE Citer.article = rl_id AND Citer.authorPriority = ii
LOOP
my_citer_string := my_citer_string || my_record2.author || ', ';
END LOOP;
END LOOP;
my_citer_string = substr(my_citer_string, '', length(my_citer_string)-1) || ';';
my_rl_line := 'Unpublished results, cited by:
RL ' || my_citer_string || '
' || my_rl_line;
END IF;
/* Category is Book */
ELSE IF table_type = 'Book'
THEN
SELECT INTO my_record Book.bookTitle, Book.editors, Book.publisher,
Book.city, Book.year, ReferenceLocationBook.volume, ReferenceLocationBook.pageFirst, ReferenceLocationBook.pageLast
FROM ReferenceLocationBook, Book
WHERE ReferenceLocationBook.referenceID = rl_id AND Book.bookID = ReferenceLocationBook.bookID;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN rl_book', rl_id;
RETURN '!ERROR: NO REF. % in the book table!';
END IF;
my_rl_line := '(IN) ' || my_record.editors || ' (eds.);
RL ' || my_record.bookTitle || ', pp.' ||
my_record.pageFirst || '-' || my_record.pageLast || ', ' || my_record.publisher ||
' (' || my_record.year || ').';
/* Category is Unpublished observations */
ELSE IF table_type = 'Unpublished observations'
THEN
SELECT INTO my_record ReferenceLocationUnpubObservations.month, ReferenceLocationUnpubObservations.year
FROM ReferenceLocationUnpubObservations
WHERE ReferenceLocationUnpubObservations.referenceID = rl_id;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN ReferenceLocationUnpubObservations', rl_id;
RETURN '!ERROR: NO REF. % in the unpublished observations table!';
END IF;
my_rl_line := 'Unpublished obseravtions ('|| get_month(my_record.month) || '- ' ||my_record.year || ').';
/* Category is Thesis */
ELSE IF table_type = 'Thesis'
THEN
SELECT INTO my_record referenceLocationThesis.year, referenceLocationThesis.institution, referenceLocationThesis.country
FROM referenceLocationThesis
WHERE referenceLocationThesis.referenceID = rl_id;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN referenceLocationThesis', rl_id;
RETURN '!ERROR: NO REF. % in the thesis table!';
END IF;
my_rl_line := 'Thesis (' || my_record.year || '), ' || my_record.institution ||
', ' || my_record.country || '.';
/* Category is Patent applictions */
ELSE IF table_type = 'Patent application'
THEN
SELECT INTO my_record referenceLocationPatent.patent_publication_number, referenceLocationPatent.date
FROM referenceLocationPatent
WHERE referenceLocationPatent.referenceID = rl_id;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN referenceLocationPatent', rl_id;
RETURN '!ERROR: NO REF. % in the patent applications table!';
END IF;
my_day := date_part('day', referenceLocationPatent.date);
my_month := date_part('month', referenceLocationPatent.date);
my_month_letter := get_month(my_month);
my_year := date_part('year', referenceLocationPatent.date);
my_rl_line := 'Patent number ' || my_record.patent_publication_number || ', ' ||
my_day || '-' || my_month_letter || '-' || my_year || '.';
/* Category is Submission */
ELSE IF table_type = 'Submission'
THEN
SELECT INTO my_record referenceLocationSubmission.month, referenceLocationSubmission.year, referenceLocationSubmission.XrefDBCode,
XrefDB.XrefDBName, XrefDB.url
FROM referenceLocationSubmission, XrefDB
WHERE referenceLocationSubmission.referenceID = rl_id AND XrefDB.XrefDBCode = referenceLocationSubmission.XrefDBCode;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN referenceLocationSubmission', rl_id;
RETURN '!ERROR: NO REF. % in the submission table!';
END IF;
my_rl_line := 'Submitted (' || get_month(my_record.month) || '-' || my_record.year || ') to the ' ||
my_record.XrefDBName || ' database.';
/* Category is OTHER */
ELSE IF table_type = 'OTHER' OR table_type = 'Personal communiction'
THEN
SELECT INTO my_record referenceLocationOther.text
FROM referenceLocationOther
WHERE referenceLocationOther.referenceID = rl_id;
IF NOT FOUND THEN
RAISE EXCEPTION 'Error calling make2db_rl_reconstruct -> NO REF. % IN referenceLocationOther', rl_id;
RETURN '!ERROR: NO REF. % in the OTHER table!';
END IF;
my_rl_line := my_record.text || '.';
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
END IF;
RETURN my_rl_line;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO SWITCH THE showFlagSwitcher on/off
-- FUNCTION TO SWITCH THE showFlagSwitcher on/off
-------------------------------------------------
-- Argument: True -> Set switch to TRUE for False showFlags and erase hidden data from public tables
-- False -> Set switch to False for False showFlags
DECLARE
my_switch ALIAS FOR $1;
my_switch_text TEXT;
my_tables TEXT;
my_table TEXT;
my_record RECORD;
BEGIN
-- List of tables containing a showFlagSwitch: (separated by a single space, *the last space is mandatory*)
-- It is preferable to list the tables in the decreasing order of dependencies (even if cascade references are on)
my_tables := 'SpotIdentificationParent* SpotDataParent* SpotEntry EntryGelImage EntryGelImage EntryGelMasTer Entry Gel ';
IF (my_switch IS NULL) THEN RETURN FALSE; END IF;
IF (my_switch) THEN
my_switch_text := 'TRUE';
ELSE
my_switch_text := 'FALSE';
END IF;
WHILE strpos(my_tables, ' ') <> 0 LOOP
my_table := substr(my_tables, 0, strpos(my_tables, ' '));
my_tables := substr(my_tables, strpos(my_tables, ' ') + 1, length(my_tables));
EXECUTE 'UPDATE ' || my_table || ' SET showFlagSwitch = ' || my_switch_text || ' WHERE showFlag IS FALSE';
-- Erase any records with a False showFlag from schema public
IF (my_switch) THEN
EXECUTE 'DELETE FROM public.' || my_table || ' WHERE showFlag IS FALSE';
END IF;
END LOOP;
RETURN TRUE;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO UPDATE INTERNAL DATA, VIEWS AND PUBLIC DATA
First argument: (0) not any update to the core schema
(1) to update the core schema views without inner data modification if inner data is not null,
(2) to update the core schema views and import the external data replacing the inner data (no modification on ACs, IDs nor descriptions)
(3) to update the core schema views and import the external data replacing the inner data (including ACs, IDs and descriptions)
Second argument: (0) to not export to the public schema,
(>0) to export all changes from the core schema to the public schema
-- FUNCTION TO UPDATE INTERNAL DATA, VIEWS AND PUBLIC DATA
----------------------------------------------------------
-- The alogrythm is:
-- if (export and not update internal) -> backup Views
-- if (export) -> switch off showFlagSwitchs
-- if (update internal) -> update internals
-- construct Views
-- if (export) -> export to public schema, switch on showFlagSwitchs
-- if (export and update internal) -> re-construct Views
-- if (export and not update internal) -> restore Views
-- First argument: (0) not any update to the core schema
-- (1) to update the core schema views without inner data modification if inner data is not null,
-- (2) to update the core schema views and import the external data replacing the inner data (no modification on IDs or descriptions)
-- (3) to update the core schema views and import the external data replacing the inner data (including IDs and descriptions)
-- Second argument: (0) to not export to the public schema,
-- (>0) to export all changes from the core schema to the public schema
DECLARE
update_internal_data ALIAS for $1;
export_to_public ALIAS for $2;
import_external_data_partial INT;
import_external_data_full INT;
my_core_schema VARCHAR(16);
my_core_table VARCHAR(256);
my_public_schema VARCHAR(16);
my_public_table VARCHAR(256);
my_record_core_tables RECORD;
my_record_container RECORD;
BEGIN
SET DATESTYLE TO 'POSTGRES, EUROPEAN';
IF (update_internal_data = 0) AND (export_to_public = 0) THEN
RAISE NOTICE 'Update: nothing to do...';
RETURN 'true';
END IF;
-- Backup Views, Switch off showFlagSwitchs
-- ######################################## --
IF (export_to_public > 0 AND update_internal_data = 0) THEN
SELECT INTO my_record_container make2db_backup_views(TRUE) AS status;
IF (my_record_container.status IS NOT TRUE) THEN
RAISE NOTICE 'Update Error: Cannot backup Views!';
RETURN 'false';
END IF;
END IF;
-- Switch off showFlagSwitchs
-- ########################## --
IF (export_to_public > 0) THEN
SELECT INTO my_record_container make2db_showFlagSwitcher (FALSE);
END IF;
-- UPDATE INTERNALS
-- ################ --
IF (update_internal_data > 0) THEN
import_external_data_partial := 0;
import_external_data_full := 0;
IF (update_internal_data > 1) THEN
import_external_data_partial := 1;
IF (update_internal_data > 2) THEN
import_external_data_full := 1;
END IF;
END IF;
-- UPDATE INTERNAL DATA:
-- *********************************************************--
-- PERFORM make2db_update_internal_primaryAC (import_external_data_full);
SELECT INTO my_record_container make2db_update_internal_primaryAC (import_external_data_full);
-- PERFORM make2db_update_internal_id (import_external_data_full);
SELECT INTO my_record_container make2db_update_internal_id (import_external_data_full);
-- PERFORM make2db_update_internal_de (import_external_data_full);
SELECT INTO my_record_container make2db_update_internal_de (import_external_data_full);
-- PERFORM make2db_update_internal_gn (import_external_data_partial);
SELECT INTO my_record_container make2db_update_internal_gn (import_external_data_partial);
-- PERFORM make2db_update_internal_kw (import_external_data_partial);
SELECT INTO my_record_container make2db_update_internal_kw (import_external_data_partial);
-- PERFORM make2db_update_internal_ec ();
SELECT INTO my_record_container make2db_update_internal_ec ();
-- PERFORM make2db_update_sp_trembl_dr ();
SELECT INTO my_record_container make2db_update_sp_trembl_dr ();
-- *********************************************************--
END IF;
-- CONSTRUCT VIEWS
-- ############### --
-- LAUNCH FULL ENTRIES CONSTRUCTION:
-- ****************************************--
-- PERFORM make2db_construct_entry('all');
SELECT INTO my_record_container make2db_construct_entry('all');
-- ****************************************--
-- BUILD PROTEINS LISTS FOR EVERY MAP:
-- **********************************--
-- PERFORM make2db_map_protein_list();
SELECT INTO my_record_container make2db_map_protein_list();
-- **********************************--
-- Export to public schema, Switch on showFlagSwitchs
-- ################################################## --
IF (export_to_public > 0) THEN
my_core_schema := 'core';
my_public_schema := 'public';
FOR my_record_core_tables IN SELECT tablename FROM pg_tables WHERE lower(schemaname) = my_core_schema
LOOP
my_core_table := my_core_schema || '.' || my_record_core_tables.tablename;
my_public_table := my_public_schema || '.' || my_record_core_tables.tablename;
IF EXISTS (SELECT tablename FROM pg_tables WHERE tablename = my_record_core_tables.tablename AND lower(schemaname) = my_public_schema)
THEN
EXECUTE 'DELETE FROM ' || my_public_table;
EXECUTE 'INSERT INTO ' || my_public_table || ' SELECT * FROM ' || my_core_table;
ELSE
RAISE NOTICE 'Data Update Failure! Could NOT FIND %', my_public_table;
RETURN 'false';
END IF;
END LOOP;
SELECT INTO my_record_container make2db_showFlagSwitcher (TRUE);
END IF;
-- RE-CONSTRUCT VIEWS
-- ################## --
IF (update_internal_data > 0 AND export_to_public > 0) THEN
-- LAUNCH FULL ENTRIES CONSTRUCTION:
-- ****************************************--
-- PERFORM make2db_construct_entry('all');
SELECT INTO my_record_container make2db_construct_entry('all');
-- ****************************************--
-- BUILD PROTEINS LISTS FOR EVERY MAP:
-- **********************************--
-- PERFORM make2db_map_protein_list();
SELECT INTO my_record_container make2db_map_protein_list();
-- **********************************--
END IF;
-- Restore Views
-- ############# --
IF (export_to_public > 0 AND update_internal_data = 0) THEN
SELECT INTO my_record_container make2db_backup_views(FALSE) AS status;
IF (my_record_container.status IS NOT TRUE) THEN
RAISE NOTICE 'Update Error: Can not restore Views!';
RETURN 'false';
END IF;
END IF;
RAISE NOTICE 'Data Updates Performed With Success!';
RETURN 'true';
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO INCORPORATE SP "DE" (description) VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE.
If argument = 0 : Replacement is performed only if the Main Entry Table contains no data or if data is *identical* to the AC.
If argument > 0 : all is replaced.
-- FUNCTION TO INCORPORATE SP "DE" (description) VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
--------------------------------------------------------------------------------------------------------------
-- If argument = 0 : Replacement is performed only if the Main Entry Table contains no data or if data is *identical to the AC
-- If argument > 0 : all is replaced
DECLARE
my_record RECORD;
my_record2 RECORD;
my_status BOOLEAN;
my_argument ALIAS for $1;
BEGIN
SET search_path TO core,common;
my_status = 'false';
FOR my_record IN SELECT Entry.AC, Entry.description FROM Entry, ExternalMainXrefData
WHERE Entry.AC = ExternalMainXrefData.AC
AND ExternalMainXrefData.uniProtDescription IS NOT NULL
AND (Entry.description != ExternalMainXrefData.uniProtDescription OR Entry.description IS NULL)
LOOP
SELECT INTO my_record2 uniProtDescription FROM ExternalMainXrefData WHERE AC = my_record.AC LIMIT 1;
IF substr(my_record2.uniProtDescription, length(my_record2.uniProtDescription), length(my_record2.uniProtDescription)+1) = '.' THEN
my_record2.uniProtDescription = substr(my_record2.uniProtDescription, 0, length(my_record2.uniProtDescription));
END IF;
IF my_argument > 0 THEN
UPDATE Entry SET description = my_record2.uniProtDescription WHERE AC = my_record.AC;
my_status = 'true';
ELSE IF my_record.description IS NULL OR my_record.description = my_record.AC THEN
UPDATE Entry SET description = my_record2.uniProtDescription WHERE AC = my_record.AC;
my_status = 'true';
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO INCORPORATE SP "EC" codes FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
-- FUNCTION TO INCORPORATE SP "EC" codes FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
-----------------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
my_record2 RECORD;
my_status BOOLEAN;
BEGIN
SET search_path TO core,common;
my_status = 'false';
-- FOR my_record IN SELECT Entry.AC FROM Entry WHERE Entry.ac NOT IN (SELECT EnzymeNomenclature.AC FROM EnzymeNomenclature)
-- The EC table is automatically updated once
-- (e.g. if does not exist initially in data), otherwise, direct manual update is required
FOR my_record IN SELECT Entry.AC FROM Entry EXCEPT SELECT EnzymeNomenclature.AC FROM EnzymeNomenclature
LOOP
IF EXISTS (SELECT uniProtEnzymeCode FROM ExternalMainXrefData WHERE AC = my_record.AC AND uniProtEnzymeCode IS NOT NULL)
THEN
SELECT INTO my_record2 uniProtEnzymeCode FROM ExternalMainXrefData WHERE AC = my_record.AC LIMIT 1;
INSERT INTO EnzymeNomenclature (AC, enzymeCode) VALUES (my_record.AC, my_record2.uniProtEnzymeCode);
my_status = 'true';
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO INCORPORATE SP "GN" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE.
If argument = 0 : Replacement is performed only if the Main Entry Table contains no data for GeneNames.
If argument > 0 : all is replaced.
-- FUNCTION TO INCORPORATE SP "GN" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
------------------------------------------------------------------------------------------------
-- If argument = 0 : Replacement is performed only if the Main Entry Table contains no data for GeneNames
-- If argument > 0 : all is replaced
DECLARE
my_record RECORD;
my_record2 RECORD;
my_status BOOLEAN;
my_argument ALIAS for $1;
BEGIN
SET search_path TO core,common;
my_status = 'false';
FOR my_record IN SELECT Entry.AC, Entry.geneNames FROM Entry, ExternalMainXrefData
WHERE Entry.AC = ExternalMainXrefData.AC
AND ExternalMainXrefData.uniProtGeneNames IS NOT NULL
AND (Entry.geneNames != ExternalMainXrefData.uniProtGeneNames OR Entry.geneNames IS NULL)
LOOP
SELECT INTO my_record2 uniProtGeneNames FROM ExternalMainXrefData WHERE AC = my_record.AC LIMIT 1;
IF substr(my_record2.uniProtGeneNames, length(my_record2.uniProtGeneNames), length(my_record2.uniProtGeneNames)+1) = '.' THEN
my_record2.uniProtGeneNames = substr(my_record2.uniProtGeneNames, 0, length(my_record2.uniProtGeneNames));
END IF;
IF my_argument > 0 THEN
UPDATE Entry SET geneNames = my_record2.uniProtGeneNames WHERE AC = my_record.AC;
my_status = 'true';
ELSE IF my_record.geneNames IS NULL THEN
UPDATE Entry SET geneNames = my_record2.uniProtGeneNames WHERE AC = my_record.AC;
my_status = 'true';
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO INCORPORATE SP "ID" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE.
If argument = 0 : Replacement is performed only if the Main Entry Table contains no data or if data is *identical* to the AC.
If argument > 0 : all is replaced.
-- FUNCTION TO INCORPORATE SP "ID" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
------------------------------------------------------------------------------------------------
-- If argument = 0 : Replacement is performed only if the Main Entry Table contains no data or if data is *identical to the AC
-- If argument > 0 : all is replaced
DECLARE
my_record RECORD;
my_record2 RECORD;
my_status BOOLEAN;
my_argument ALIAS for $1;
BEGIN
SET search_path TO core,common;
my_status = 'false';
FOR my_record IN SELECT Entry.AC, Entry.ID FROM Entry, ExternalMainXrefData
WHERE Entry.AC = ExternalMainXrefData.AC
AND ExternalMainXrefData.uniProtID IS NOT NULL
AND (Entry.ID != ExternalMainXrefData.uniProtID OR Entry.ID IS NULL)
LOOP
SELECT INTO my_record2 uniProtID FROM ExternalMainXrefData WHERE AC = my_record.AC LIMIT 1;
IF NOT EXISTS (SELECT ID FROM ENTRY WHERE ID = my_record2.uniProtID LIMIT 1) -- ID should remain unique in Entry
THEN
IF my_argument > 0 THEN
UPDATE Entry SET ID = my_record2.uniProtID WHERE AC = my_record.AC;
my_status = 'true';
ELSE IF my_record.ID IS NULL OR my_record.ID = my_record.AC THEN
UPDATE Entry SET ID = my_record2.uniProtID WHERE AC = my_record.AC;
my_status = 'true';
END IF;
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO INCORPORATE SP "KW" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE.
If argument = 0 : Replacement is performed only if the Main Entry Table contains no data for keywords.
If argument > 0 : all is replaced (use only this format to keep keywords Swiss-Prot compliant).
-- FUNCTION TO INCORPORATE SP "KW" VALUES FROM THE EXTERNAL DATA TABLE INTO THE MAIN ENTRY TABLE
------------------------------------------------------------------------------------------------
-- If argument = 0 : Replacement is performed only if the Main Entry Table contains no data for keywords
-- If argument > 0 : all is replaced (use only this format to keep keywords Swiss-Prot compliant)
DECLARE
my_record RECORD;
my_record2 RECORD;
my_status BOOLEAN;
my_argument ALIAS for $1;
BEGIN
SET search_path TO core,common;
my_status = 'false';
FOR my_record IN SELECT Entry.AC, Entry.keywords FROM Entry, ExternalMainXrefData
WHERE Entry.AC = ExternalMainXrefData.AC
AND ExternalMainXrefData.uniProtCategoryKeywords IS NOT NULL
AND (Entry.keywords != ExternalMainXrefData.uniProtCategoryKeywords OR Entry.keywords IS NULL)
LOOP
SELECT INTO my_record2 uniProtCategoryKeywords FROM ExternalMainXrefData WHERE AC = my_record.AC LIMIT 1;
IF substr(my_record2.uniProtCategoryKeywords, length(my_record2.uniProtCategoryKeywords), length(my_record2.uniProtCategoryKeywords)+1) = '.' THEN
my_record2.uniProtCategoryKeywords = substr(my_record2.uniProtCategoryKeywords, 0, length(my_record2.uniProtCategoryKeywords));
END IF;
IF my_argument > 0 THEN
UPDATE Entry SET keywords = my_record2.uniProtCategoryKeywords WHERE AC = my_record.AC;
my_status = 'true';
ELSE IF my_record.keywords IS NULL THEN
UPDATE Entry SET keywords = my_record2.uniProtCategoryKeywords WHERE AC = my_record.AC;
my_status = 'true';
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO UPDATE LOCAL PRIMARY ACs REGARDING UNIPROT PRIMARY ACs. THE OLD ACs THEN BECOME LOCAL SECONDARY ACs.
If argument > 0 : All ACs are updated to their corresponding UniProt Primary AC.
If argument = 0 : No AC replacement. Only a potential new local secondary AC (corresponding to the Primary UniProt AC) is added.
-- FUNCTION TO UPDATE PRIMARY AC FROM THE EXTERNAL DATA TABLE REGARDING THE MAIN ENTRY TABLE
--------------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
my_status BOOLEAN;
my_argument ALIAS for $1;
BEGIN
SET search_path TO core,common;
my_status = 'false';
FOR my_record IN SELECT ExternalMainXrefData.AC, ExternalMainXrefData.uniProtAC, ExternalMainXrefData.uniProtID
FROM ExternalMainXrefData
WHERE ExternalMainXrefData.AC = ANY (ExternalMainXrefData.uniProtSecondaryAC)
LOOP
IF NOT EXISTS (SELECT AC FROM Entry WHERE AC = my_record.uniProtAC)
THEN
IF my_argument = 0 THEN
IF NOT EXISTS (SELECT * FROM SecondaryAC WHERE secondaryAC = my_record.uniProtAC AND AC = my_record.AC) THEN
INSERT INTO SecondaryAC (secondaryAC, AC) VALUES (my_record.uniProtAC, my_record.AC);
my_status = 'true';
END IF;
ELSE
DELETE FROM SecondaryAC WHERE secondaryAC = my_record.uniProtAC AND AC = my_record.AC;
UPDATE Entry SET AC = my_record.uniProtAC WHERE AC = my_record.AC;
INSERT INTO SecondaryAC (secondaryAC, AC) VALUES (my_record.AC, my_record.uniProtAC);
IF NOT EXISTS (SELECT ID FROM Entry WHERE ID = my_record.uniProtID)
THEN
UPDATE Entry SET ID = my_record.uniProtID WHERE AC = my_record.AC;
END IF;
my_status = 'true';
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO UPDATE EntryXrefDB content regarding ExternalMainXrefData for Swiss-Prot & TrEMBL
-- FUNCTION TO UPDATE EntryXrefDB content regarding ExternalMainXrefData for Swiss-Prot & TrEMBL
------------------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
my_status BOOLEAN;
BEGIN
SET search_path TO core,common;
my_status = 'false';
-- for more consistency, add a rule clause (AC, 1 or 2) in EntryXrefDB table / 1 is SP, 2 is TrEMBL
FOR my_record IN SELECT * FROM ExternalMainXrefData
LOOP
IF my_record.uniProtAC IS NOT NULL AND my_record.SPorTrEMBL THEN -- Swiss-Prot reference
IF EXISTS (SELECT AC FROM EntryXrefDB WHERE AC = my_record.AC AND (XrefDBCode = 1 OR XrefDBCode = 2) LIMIT 1)
THEN
DELETE FROM EntryXrefDB WHERE AC = my_record.AC AND (XrefDBCode = 1 OR XrefDBCode = 2);
END IF;
INSERT INTO EntryXrefDB (AC, XrefDBCode, XrefPrimaryIdentifier, XrefSecondaryIdentifier)
values (my_record.AC, 1, my_record.uniProtAC, my_record.uniProtID);
my_status = 'true';
ELSE IF my_record.uniProtAC IS NOT NULL AND NOT my_record.SPorTrEMBL THEN -- TrEMBL reference
IF EXISTS (SELECT AC FROM EntryXrefDB WHERE AC = my_record.AC AND (XrefDBCode = 1 OR XrefDBCode = 2) LIMIT 1)
THEN
DELETE FROM EntryXrefDB
-- test XrefDBCode 1, as automatically added DR for AC matching SP pattern assume the reference to be SP
WHERE AC = my_record.AC AND (XrefDBCode = 1 OR XrefDBCode = 2);
END IF;
INSERT INTO EntryXrefDB (AC, XrefDBCode, XrefPrimaryIdentifier, XrefSecondaryIdentifier)
values (my_record.AC, 2, my_record.uniProtAC, my_record.uniProtID);
my_status = 'true';
END IF;
END IF;
END LOOP;
RETURN my_status;
END;
Returns: boolean
Language: PLPGSQL
FUNCTION TO UPDATE ENTRY VERSIONS WHEN annotationChanged IS TRUE.
If argument is TRUE => Update Entry View
No version will hold a 0
-- FUNCTION TO UPDATE ENTRY VERSIONS WHEN annotationChanged IS TRUE
-------------------------------------------------------------------
-- Argument: True -> update entry view
DECLARE
my_update_view ALIAS FOR $1;
my_record RECORD;
my_record_container RECORD;
BEGIN
SET DATESTYLE TO 'POSTGRES, EUROPEAN';
-- initialisation part: we do not want any version to be zero (min 1) / if annotationChanged is true, the increment is treated after
-- (this loop will be mainly executed at the beginning of the database life)
FOR my_record IN
SELECT AC FROM EntryVersionParent* WHERE version = 0 AND annotationChanged IS FALSE
LOOP
UPDATE EntryVersionParent* SET version = 1 WHERE version = 0 AND annotationChanged IS FALSE;
IF (my_update_view IS TRUE) THEN
SELECT INTO my_record_container make2db_construct_entry(my_record.AC); -- function defined in the final views
END IF;
END LOOP;
SELECT INTO my_record AC FROM EntryVersionParent* WHERE EntryVersionParent.annotationChanged = TRUE LIMIT 1;
IF NOT FOUND THEN
RETURN FALSE;
END IF;
IF (my_update_view IS FALSE OR my_update_view IS NULL) THEN
UPDATE EntryVersionParent SET version = version + 1, versionDate = CURRENT_DATE, annotationChanged = FALSE
WHERE annotationChanged = TRUE;
RETURN TRUE;
END IF;
FOR my_record IN
SELECT AC FROM EntryVersionParent* WHERE annotationChanged = TRUE
LOOP
UPDATE EntryVersionParent* SET version = version + 1,
versionDate = CURRENT_DATE, annotationChanged = FALSE
WHERE annotationChanged = TRUE AND AC = my_record.AC;
SELECT INTO my_record_container core.make2db_construct_entry(my_record.AC); -- function defined in the final views
END LOOP;
RETURN TRUE;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON Analyte: Track the parental sampleID for all cyclic - children - Analytes from their direct parent
-- TRIGGER ON Analyte: Track the parental sampleID for all cyclic - children - Analytes from their direct parent
----------------------------------------------------------------------------------------------------------------
-- This will update sampleID for children *once* when entered. If parent changes, sampleID will not be synchronized!
DECLARE
my_record RECORD;
BEGIN
IF new.analyteParentID IS NOT NULL THEN
SELECT INTO my_record sampleID FROM Analyte WHERE analyteID = new.analyteParentID;
new.sampleID = my_record.sampleID;
END IF;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON common.Database: Insert into (or update) the Release Table according to the last update release data on common.Database
-- TRIGGER ON common.Database: Insert into (or update) the Release Table accordingly
------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
BEGIN
SELECT INTO my_record * FROM Release WHERE releaseNum = new.databaseRelease AND subRelease = new.databaseSubRelease;
IF FOUND THEN -- side updates are performed over the database table!
-- UPDATE Release SET releaseDate = new.databaseReleaseDate
-- WHERE releaseNum = new.databaseRelease AND subRelease = new.databaseSubRelease;
ELSE
INSERT INTO Release VALUES (new.databaseRelease, new.databaseSubRelease, new.databaseReleaseDate);
END IF;
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON ENTRY: Make sure AC's are in upper case (for case insensitivity)
-- TRIGGER ON ENTRY: Make sure AC's are in upper case (for case insensitivity)
------------------------------------------------------------------------------
BEGIN
new.AC = upper(new.AC);
new.ID = upper(new.ID);
new.description = common.substitute_text(new.description, ' precursor', '');
IF new.AC = 'UNIDENTIFIED_SPOTS' THEN
new.showFlag = 'false';
-- new.showFlagSwitch = 'false';
END IF;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON Entry: Set *AnnotationChanged to true when appropriate
-- TRIGGER ON Entry: Set *AnnotationChanged to true when appropriate
---------------------------------------------------------------------
BEGIN -- We need to act only when the update changes effectively some selected values
IF (new.AC <> old.AC OR new.ID <> old.ID OR new.entryClass <> old.entryClass OR
new.description <> old.description OR new.geneNames <> old.geneNames OR new.keywords <> old.keywords OR
new.organismID <> old.organismID OR new.organismStrain <> old.organismStrain)
THEN UPDATE core.EntryVersionGeneral SET annotationChanged = 'true' WHERE AC = new.AC;
END IF;
IF (new.identMethod <> old.identMethod)
THEN UPDATE core.EntryVersion2D SET annotationChanged = 'true' WHERE AC = new.AC;
END IF;
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON Entry, DEPRECATED!: Synchronize Version and Annotation Flags between Maps and General Updates
-- TRIGGER ON Entry: Synchronize Version and Annotation Flags between Maps and General Updates
----------------------------------------------------------------------------------------------
BEGIN
--IF new.releaseMapUpdate < new.releaseCreation THEN
-- new.releaseMapUpdate = new.releaseCreation;
--END IF;
--IF new.releaseUpdate < new.releaseMapUpdate THEN
-- new.releaseUpdate = new.releaseMapUpdate;
--END IF;
--IF new.mapAnnotationChanged IS TRUE THEN
-- new.entryAnnotationChanged = 'true';
--END IF;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON EntryVersionParent*: For updates, set annotationChanged to TRUE
-- TRIGGER ON EntryVersionParent*: For updates, set annotationChanged to TRUE
-----------------------------------------------------------------------------
BEGIN
-- new.version = old.version + 1;
-- new.versionDate = CURRENT_DATE;
new.annotationChanged = TRUE;
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON EntryXrefDB: Set *AnnotationChanged to true when appropriate
-- TRIGGER ON EntryXrefDB: Set Entry.*AnnotationChanged to true when appropriate
---------------------------------------------------------------------------------
BEGIN -- We need to act only when the update changes effectively some selected values
IF (new.XrefDBCode <> old.XrefDBCode OR new.XrefPrimaryIdentifier <> old.XrefPrimaryIdentifier OR
new.XrefSecondaryIdentifier <> old.XrefSecondaryIdentifier OR new.XrefTertiaryIdentifier <> old.XrefTertiaryIdentifier)
THEN UPDATE core.EntryVersionGeneral SET annotationChanged = 'true' WHERE AC = new.AC;
END IF;
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON EntryXrefDBDynamic: Skip a Record on EntryXrefDBDynamic if same Xref exists on EntryXrefDB (update the later)
-- TRIGGER ON EntryXrefDBDynamic: Skip a Record if same Xref exists on EntryXrefDB (update the later)
------------------------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
BEGIN
SELECT INTO my_record XrefDBCode FROM XrefDB WHERE upper(XrefDBName) =
(SELECT upper(XrefDBName) FROM XrefDBDynamic WHERE XrefDBCode = new.XrefDBCode LIMIT 1);
IF my_record.XrefDBCode IS NOT NULL THEN
IF EXISTS (SELECT * FROM EntryXrefDB WHERE AC = new.AC AND XrefDBCode = my_record.XrefDBCode
AND XrefPrimaryIdentifier = new.XrefPrimaryIdentifier AND activated IS TRUE) THEN
UPDATE EntryXrefDB SET XrefSecondaryIdentifier = new.XrefSecondaryIdentifier WHERE
AC = new.AC AND XrefDBCode = my_record.XrefDBCode AND XrefPrimaryIdentifier = new.XrefPrimaryIdentifier;
RETURN NULL;
ELSE
RETURN new;
END IF;
ELSE
RETURN new;
END IF;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON GEL: Upper case shortName and replace melanieGeneratedID by shortName if melanieGeneratedID is NULL
-- TRIGGER ON GEL: Upper case shortName and replace melanieGeneratedID by shortName if melanieGeneratedID is NULL
------------------------------------------------------------------------------------------------------------------
DECLARE
my_record RECORD;
my_last_spot VARCHAR(16);
BEGIN
new.shortName = upper(new.shortName);
IF new.melanieGeneratedID IS NOT NULL AND new.melanieGeneratedID <> '' THEN
RETURN new;
END IF;
new.melanieGeneratedID = current_database() || ':' || new.shortName;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON GelTissueSP: Upper case SP tissue names
-- TRIGGER ON GelTissueSP: Upper case SP tissue names
-----------------------------------------------------
BEGIN
new.tissueSPName = upper(new.tissueSPName);
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER OON Tables containing ShowFlags: Turn showFlagSwitch to TRUE if showFlag becomes TRUE
-- TRIGGER ON Tables containing ShowFlags: Turn showFlagSwitch to TRUE if showFlag becomes TRUE
-----------------------------------------------------------------------------------------------
BEGIN
IF (new.showFlag IS TRUE) THEN new.showFlagSwitch = 'true';
END IF;
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON Spot: Insert a Defined & Increased SPOT/BAND ID if ID IS Not Defined
-- TRIGGER ON Spot: Insert a Defined & Increased SPOT/BAND ID if ID IS Not Defined
----------------------------------------------------------------------------------
-- The ID starts with 1/2D-X100000 and is then incremental (hexadecimal)
DECLARE
my_record RECORD;
my_last_spot VARCHAR(16);
BEGIN
IF new.spotID <> '' THEN RETURN new;
END IF;
IF new.pI IS NOT NULL THEN
SELECT INTO my_record spotID FROM Spot
WHERE pI IS NOT NULL AND spotID ~ '^2D-X' ORDER BY 1 DESC LIMIT 1;
IF FOUND THEN my_last_spot := '2D-X' || int_to_hex(hex_to_int(substr(my_record.spotID, 5)) + 1);
ELSE my_last_spot := '2D-X100000';
END IF;
ELSE
SELECT INTO my_record spotID FROM Spot
WHERE pI IS NULL AND spotID ~ '^1D-X' ORDER BY 1 DESC LIMIT 1;
IF FOUND THEN my_last_spot := '1D-X' || int_to_hex(hex_to_int(substr(my_record.spotID, 5)) + 1);
ELSE my_last_spot := '1D-X100000';
END IF;
END IF;
new.spotID = my_last_spot;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON SpotDataParent*: Force dataExpID to hold nextval(make2db_spotDataExp)
-- TRIGGER ON SpotDataParent*: Force dataExpID to hold nextval(make2db_spotDataExp)
-----------------------------------------------------------------------------------
BEGIN
new.dataExpID = nextval(make2db_spotDataExp);
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON SpotIdentificationParent*: Force identificationID to hold nextval(make2db_spotIdentification)
-- TRIGGER ON SpotIdentificationParent*: Force identificationID to hold nextval(make2db_spotIdentification)
-----------------------------------------------------------------------------------------------------------
BEGIN
new.identificationID = nextval(make2db_spotIdentification);
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON TissueSP: Upper case SP tissue names
-- TRIGGER ON TissueSP: Upper case SP tissue names
--------------------------------------------------
BEGIN
new.tissueSPName = upper(new.tissueSPName);
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON TissueSPAliase: Upper case SP tissue names
-- TRIGGER ON TissueSPAliase: Upper case SP tissue names
--------------------------------------------------------
BEGIN
new.tissueSPName = upper(new.tissueSPName);
new.Alias = upper(new.Alias);
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON TissueSPTissueMapping: Upper case SP tissue names
-- TRIGGER ON TissueSPTissueMapping: Upper case SP tissue names
---------------------------------------------------------------
BEGIN
new.tissueSPName = upper(new.tissueSPName);
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
-- Trigger function to automatically insert 'userStamp' and 'update' time values
-- This trigger is applied on every core table
BEGIN
new.userstamp = USER; new.update = now();
return new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON XrefDB: Make Database name (XrefDBName) case-insensitive
-- TRIGGER ON XrefDB: Make Database name (XrefDBName) case-insensitive
----------------------------------------------------------------------
DECLARE
my_record RECORD;
my_last_spot VARCHAR(16);
my_max_iteration INT2;
my_new_db_name VARCHAR;
BEGIN
my_max_iteration = 99;
IF EXISTS (SELECT * FROM core.XrefDB WHERE lower(XrefDBName) = lower(new.XrefDBName)) THEN
RAISE NOTICE 'INSERTING AN ALREADY EXISTING Database Name (%) in XrefDB: This field should be case-insensitive!',
new.XrefDBName;
FOR my_iteration IN 1..my_max_iteration
LOOP
my_new_db_name = new.XrefDBName || '_' || my_iteration::VARCHAR;
IF NOT EXISTS (SELECT * FROM core.XrefDB WHERE lower(XrefDBName) = lower(my_new_db_name)) THEN
new.XrefDBName = my_new_db_name;
RAISE NOTICE 'The database name has been changed to: %', new.XrefDBName;
RETURN new;
END IF;
END LOOP;
RAISE EXCEPTION 'This database name has already been modified % times!', my_max_iteration;
END IF;
RETURN new;
END;
Returns: "trigger"
Language: PLPGSQL
TRIGGER ON XrefDB: Make Database name (XrefDBName) case-insensitive
-- TRIGGER ON XrefDB: Make Database name (XrefDBName) case-insensitive
----------------------------------------------------------------------
DECLARE
my_record RECORD;
my_last_spot VARCHAR(16);
my_max_iteration INT2;
my_new_db_name VARCHAR;
BEGIN
my_max_iteration = 99;
IF EXISTS (SELECT * FROM core.XrefDBDynamic WHERE lower(XrefDBName) = lower(new.XrefDBName)) THEN
RAISE NOTICE 'INSERTING AN ALREADY EXISTING Database Name (%) in XrefDB: This field should be case-insensitive!',
new.XrefDBName;
FOR my_iteration IN 1..my_max_iteration
LOOP
my_new_db_name = new.XrefDBName || '_' || my_iteration::VARCHAR;
IF NOT EXISTS (SELECT * FROM core.XrefDBDynamic WHERE lower(XrefDBName) = lower(my_new_db_name)) THEN
new.XrefDBName = my_new_db_name;
RAISE NOTICE 'The database name has been changed to: %', new.XrefDBName;
RETURN new;
END IF;
END LOOP;
RAISE EXCEPTION 'This database name has already been modified % times!', my_max_iteration;
END IF;
RETURN new;
END;
Schema log
log.analyte Structure
| F-Key |
Name |
Type |
Description |
|
|
analyteid |
integer |
|
|
|
sampleid |
integer |
|
|
|
analytepreparationid |
integer |
|
|
|
description |
text |
|
|
|
analyteparentid |
integer |
|
|
|
fromanalyzablesource |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.analyte Constraints
| Name |
Constraint |
| analyte_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| analyte_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.analytepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
analytepreparationid |
integer |
|
|
|
preparationprotocol |
text |
|
|
|
uri |
character varying(4096) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.analytepreparation Constraints
| Name |
Constraint |
| analytepreparation_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| analytepreparation_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.analyzable Structure
| F-Key |
Name |
Type |
Description |
|
|
analyzableid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.analyzable Constraints
| Name |
Constraint |
| analyzable_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| analyzable_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.author Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
|
|
|
article |
integer |
|
|
|
authorpriority |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.author Constraints
| Name |
Constraint |
| author_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| author_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.authorgroup Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
|
|
|
article |
integer |
|
|
|
authorpriority |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.authorgroup Constraints
| Name |
Constraint |
| authorgroup_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| authorgroup_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.authorparent Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
|
|
|
article |
integer |
|
|
|
authorpriority |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.authorparent Constraints
| Name |
Constraint |
| authorparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| authorparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.biologicalprocess Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
goid |
character varying(32) |
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.biologicalprocess Constraints
| Name |
Constraint |
| biologicalprocess_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| biologicalprocess_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.biosource Structure
| F-Key |
Name |
Type |
Description |
|
|
biosourceid |
integer |
|
|
|
studygroupid |
integer |
|
|
|
biosourceinformationid |
integer |
|
|
|
biosourcepreparationid |
integer |
|
|
|
description |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.biosource Constraints
| Name |
Constraint |
| biosource_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| biosource_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.biosourceinformation Structure
| F-Key |
Name |
Type |
Description |
|
|
biosourceinformationid |
integer |
|
|
|
organismid |
integer |
|
|
|
organismstrain |
character varying(256) |
|
|
|
straindetailsdescription |
text |
|
|
|
individualscount |
character varying(256) |
|
|
|
genotype |
character varying(16) |
|
|
|
developmentalstage |
character varying(256) |
|
|
|
anatomy |
character varying(256) |
|
|
|
tissueid |
integer |
|
|
|
cell |
character varying(256) |
|
|
|
cellline |
character varying(256) |
|
|
|
measuredproperties |
text |
|
|
|
environmet |
character varying(256) |
|
|
|
treatment |
text |
|
|
|
phenotype |
text |
|
|
|
behaviour |
text |
|
|
|
pathology |
text |
|
|
|
provider |
character varying(256) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.biosourceinformation Constraints
| Name |
Constraint |
| biosourceinformation_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| biosourceinformation_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.biosourcepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
biosourcepreparationid |
integer |
|
|
|
preparationprotocol |
text |
|
|
|
uri |
character varying(4096) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.biosourcepreparation Constraints
| Name |
Constraint |
| biosourcepreparation_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| biosourcepreparation_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.book Structure
| F-Key |
Name |
Type |
Description |
|
|
bookid |
integer |
|
|
|
booktitle |
character varying(256) |
|
|
|
editors |
character varying(256) |
|
|
|
publisher |
character varying(128) |
|
|
|
city |
character varying(64) |
|
|
|
year |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.book Constraints
| Name |
Constraint |
| book_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| book_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.cellularcomponent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
goid |
character varying(32) |
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.cellularcomponent Constraints
| Name |
Constraint |
| cellularcomponent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| cellularcomponent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.citer Structure
| F-Key |
Name |
Type |
Description |
|
|
author |
character varying(1024) |
|
|
|
article |
integer |
|
|
|
authorpriority |
smallint |
|
|
|
unpublished |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.citer Constraints
| Name |
Constraint |
| citer_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| citer_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.commententry2d Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
|
|
|
geldimension |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.commententry2d Constraints
| Name |
Constraint |
| commententry2d_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| commententry2d_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.commententryfreetext Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.commententryfreetext Constraints
| Name |
Constraint |
| commententryfreetext_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| commententryfreetext_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.commententryparent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
commenttopicid |
integer |
|
|
|
commentfreetext |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.commententryparent Constraints
| Name |
Constraint |
| commententryparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| commententryparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.commenttopic Structure
| F-Key |
Name |
Type |
Description |
|
|
commenttopicid |
integer |
|
|
|
commenttopicname |
character varying(64) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.commenttopic Constraints
| Name |
Constraint |
| commenttopic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| commenttopic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.contact Structure
| F-Key |
Name |
Type |
Description |
|
|
contactid |
integer |
|
|
|
name |
character varying(256) |
|
|
|
email |
character varying(256) |
|
|
|
institution |
character varying(256) |
|
|
|
address |
text |
|
|
|
remark |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.contact Constraints
| Name |
Constraint |
| contact_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| contact_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.dynamicremotemake2ddbinterface Structure
| F-Key |
Name |
Type |
Description |
|
|
interfaceid |
integer |
|
|
|
interfaceuri |
text |
|
|
|
dbnumber |
integer |
|
|
|
dbname |
character varying(128) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.dynamicremotemake2ddbinterface Constraints
| Name |
Constraint |
| dynamicremotemake2ddbinterface_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| dynamicremotemake2ddbinterface_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entry Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
id |
character varying(32) |
|
|
|
entryclass |
character varying(32) |
|
|
|
identmethod |
character varying(16) |
|
|
|
description |
text |
|
|
|
releasecreation |
integer |
|
|
|
subreleasecreation |
integer |
|
|
|
genenames |
character varying(1024) |
|
|
|
keywords |
character varying(1024) |
|
|
|
organismid |
integer |
|
|
|
organismstrain |
character varying(256) |
|
|
|
entrychecksum |
character(16) |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entry Constraints
| Name |
Constraint |
| entry_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entry_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entrygelimage Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
gelid |
integer |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entrygelimage Constraints
| Name |
Constraint |
| entrygelimage_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entrygelimage_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entrygelmaster Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
gelid |
integer |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entrygelmaster Constraints
| Name |
Constraint |
| entrygelmaster_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entrygelmaster_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entrygene Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
geneid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entrygene Constraints
| Name |
Constraint |
| entrygene_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entrygene_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entrytheoreticalpimw Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
modifiedproteindescription |
text |
|
|
|
theoreticalpi |
numeric(4,2) |
|
|
|
theoreticalmw |
integer |
|
|
|
algorithmoriginandversion |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entrytheoreticalpimw Constraints
| Name |
Constraint |
| entrytheoreticalpimw_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entrytheoreticalpimw_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryversion2d Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
version |
integer |
|
|
|
versiondate |
date |
|
|
|
annotationchanged |
boolean |
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryversion2d Constraints
| Name |
Constraint |
| entryversion2d_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryversion2d_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryversiongeneral Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
version |
integer |
|
|
|
versiondate |
date |
|
|
|
annotationchanged |
boolean |
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryversiongeneral Constraints
| Name |
Constraint |
| entryversiongeneral_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryversiongeneral_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryversionparent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
version |
integer |
|
|
|
versiondate |
date |
|
|
|
annotationchanged |
boolean |
|
|
|
annotationchecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryversionparent Constraints
| Name |
Constraint |
| entryversionparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryversionparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryxrefdb Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
xrefdbcode |
integer |
|
|
|
xrefprimaryidentifier |
character varying(32) |
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryxrefdb Constraints
| Name |
Constraint |
| entryxrefdb_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryxrefdb_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryxrefdbdynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
xrefdbcode |
integer |
|
|
|
xrefprimaryidentifier |
character varying(32) |
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryxrefdbdynamic Constraints
| Name |
Constraint |
| entryxrefdbdynamic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryxrefdbdynamic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.entryxrefdbparent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
xrefdbcode |
integer |
|
|
|
xrefprimaryidentifier |
character varying(32) |
|
|
|
xrefsecondaryidentifier |
character varying(1024) |
|
|
|
xreftertiaryidentifier |
character varying(1024) |
|
|
|
xrefotheridentifiers |
character varying(1024) |
|
|
|
activated |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.entryxrefdbparent Constraints
| Name |
Constraint |
| entryxrefdbparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| entryxrefdbparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.enzymenomenclature Structure
| F-Key |
Name |
Type |
Description |
|
|
enzymecode |
character varying(16) |
|
|
|
ac |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.enzymenomenclature Constraints
| Name |
Constraint |
| enzymenomenclature_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| enzymenomenclature_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.externalmainxrefdata Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
uniprotextractiondate |
date |
|
|
|
uniprotac |
character varying(32) |
|
|
|
uniprotsecondaryac |
character varying(32)[] |
|
|
|
uniprotid |
character varying(32) |
|
|
|
uniprotversion |
numeric(5,2) |
|
|
|
uniprotentryincorporateddate |
date |
|
|
|
uniprotsequpdate |
date |
|
|
|
uniprotsequpversion |
smallint |
|
|
|
uniprotentryupdate |
date |
|
|
|
uniprotentryupversion |
smallint |
|
|
|
uniprotdescription |
text |
|
|
|
uniprotenzymecode |
character varying(16) |
|
|
|
uniprotgenenames |
character varying(1024) |
|
|
|
uniprotorganelleplasmid |
character varying(256) |
|
|
|
uniprotcategorykeywords |
character varying(1024) |
|
|
|
uniprotxrefs |
character varying(1024)[] |
|
|
|
sportrembl |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.externalmainxrefdata Constraints
| Name |
Constraint |
| externalmainxrefdata_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| externalmainxrefdata_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.gel Structure
| F-Key |
Name |
Type |
Description |
|
|
gelid |
integer |
|
|
|
melaniegeneratedid |
character varying(64) |
|
|
|
shortname |
character varying(32) |
|
|
|
fullname |
character varying(256) |
|
|
|
dimension |
smallint |
|
|
|
startmw |
bigint |
|
|
|
endmw |
bigint |
|
|
|
startpi |
numeric(4,2) |
|
|
|
endpi |
numeric(4,2) |
|
|
|
organismid |
integer |
|
|
|
organismstrain |
character varying(256) |
|
|
|
gelparentid |
integer |
|
|
|
gelpreparationid |
integer |
|
|
|
gelinformaticsid |
integer |
|
|
|
biosourceinformationid |
integer |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.gel Constraints
| Name |
Constraint |
| gel_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| gel_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.gelcomputabledynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
databasename |
character varying(64) |
|
|
|
gelshortname |
character varying(32) |
|
|
|
gelfullname |
character varying(256) |
|
|
|
organismspecies |
text |
|
|
|
taxonomycode |
integer |
|
|
|
gelcomputableurl |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.gelcomputabledynamic Constraints
| Name |
Constraint |
| gelcomputabledynamic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| gelcomputabledynamic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.geldynamic Structure
| F-Key |
Name |
Type |
Description |
|
|
databasename |
character varying(64) |
|
|
|
gelshortname |
character varying(32) |
|
|
|
gelfullname |
character varying(256) |
|
|
|
organismspecies |
text |
|
|
|
taxonomycode |
integer |
|
|
|
tissuename |
character varying(256) |
|
|
|
tissuespname |
character varying(256) |
|
|
|
gelurl |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.geldynamic Constraints
| Name |
Constraint |
| geldynamic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| geldynamic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.gelimage Structure
| F-Key |
Name |
Type |
Description |
|
|
gelid |
integer |
|
|
|
masterimage |
oid |
|
|
|
imageurl |
text |
|
|
|
imagepath |
text |
|
|
|
imagetype |
character varying(3) |
|
|
|
smallimageurl |
text |
|
|
|
smallimagepath |
text |
|
|
|
smallimagetype |
character varying(3) |
|
|
|
xpixelsize |
smallint |
|
|
|
ypixelsize |
smallint |
|
|
|
xratio |
numeric(6,4) |
|
|
|
yratio |
numeric(6,4) |
|
|
|
xpixelshift |
smallint |
|
|
|
ypixelshift |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.gelimage Constraints
| Name |
Constraint |
| gelimage_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| gelimage_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.gelinformatics Structure
| F-Key |
Name |
Type |
Description |
|
|
gelinformaticsid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
informaticsdocument |
text |
|
|
|
informaticsdescription |
text |
|
|
|
soft |
text |
|
|
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.gelinformatics Constraints
| Name |
Constraint |
| gelinformatics_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| gelinformatics_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.gelpreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
gelpreparationid |
integer |
|
|
|
analyteid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
preparationdocument |
text |
|
|
|
preparationdescription |
text |
|
|
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.gelpreparation Constraints
| Name |
Constraint |
| gelpreparation_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| gelpreparation_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.geltissuesp Structure
| F-Key |
Name |
Type |
Description |
|
|
gelid |
integer |
|
|
|
tissuespname |
character varying(256) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.geltissuesp Constraints
| Name |
Constraint |
| geltissuesp_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| geltissuesp_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.genename Structure
| F-Key |
Name |
Type |
Description |
|
|
geneid |
integer |
|
|
|
genename |
character varying(16) |
|
|
|
organismid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.genename Constraints
| Name |
Constraint |
| genename_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| genename_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.geneontologyparent Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
goid |
character varying(32) |
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.geneontologyparent Constraints
| Name |
Constraint |
| geneontologyparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| geneontologyparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.geneorderedlocus Structure
| F-Key |
Name |
Type |
Description |
|
|
geneid |
integer |
|
|
|
orderedlocusname |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.geneorderedlocus Constraints
| Name |
Constraint |
| geneorderedlocus_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| geneorderedlocus_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.geneorf Structure
| F-Key |
Name |
Type |
Description |
|
|
geneid |
integer |
|
|
|
orfname |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.geneorf Constraints
| Name |
Constraint |
| geneorf_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| geneorf_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.generaltopicdefinition Structure
| F-Key |
Name |
Type |
Description |
|
|
generaltopicid |
integer |
|
|
|
topicname |
character varying(64) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.generaltopicdefinition Constraints
| Name |
Constraint |
| generaltopicdefinition_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| generaltopicdefinition_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.generaltopicentrydata Structure
| F-Key |
Name |
Type |
Description |
|
|
topicdataid |
integer |
|
|
|
generaltopicid |
integer |
|
|
|
topicdatatext |
text |
|
|
|
allreferences |
integer[] |
|
|
|
ambiguousreference |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.generaltopicentrydata Constraints
| Name |
Constraint |
| generaltopicentrydata_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| generaltopicentrydata_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.genesynonym Structure
| F-Key |
Name |
Type |
Description |
|
|
geneid |
integer |
|
|
|
synonym |
character varying(16) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.genesynonym Constraints
| Name |
Constraint |
| genesynonym_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| genesynonym_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.journal Structure
| F-Key |
Name |
Type |
Description |
|
|
journalid |
integer |
|
|
|
journalname |
character varying(256) |
|
|
|
url |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.journal Constraints
| Name |
Constraint |
| journal_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| journal_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.make2ddbtool Structure
| F-Key |
Name |
Type |
Description |
|
|
version |
numeric(4,2) |
|
|
|
subversion |
character varying(64) |
|
|
|
versiondate |
date |
|
|
|
postgresqlversion |
text |
|
|
|
action |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.make2ddbtool Constraints
| Name |
Constraint |
| make2ddbtool_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| make2ddbtool_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.mappingtopicdefinition Structure
| F-Key |
Name |
Type |
Description |
|
|
mappingtechnique |
character varying(8) |
|
|
|
techniquedescription |
character varying(256) |
|
|
|
containingregexp |
text |
|
|
|
excludingregexp |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.mappingtopicdefinition Constraints
| Name |
Constraint |
| mappingtopicdefinition_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| mappingtopicdefinition_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.molecularfunction Structure
| F-Key |
Name |
Type |
Description |
|
|
ac |
character varying(32) |
|
|
|
goid |
character varying(32) |
|
|
|
goname |
character varying(256) |
|
|
|
gosynoymsnames |
character varying(1024) |
|
|
|
godefinition |
character varying(1024) |
|
|
|
lastupdate |
timestamp without time zone |
|
|
|
mappedenzymeclassification |
character varying(16) |
|
|
|
mappedtransportclassification |
character varying(16) |
|
|
|
goparents |
character varying(32)[] |
|
|
|
gochildren |
character varying(32)[] |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.molecularfunction Constraints
| Name |
Constraint |
| molecularfunction_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| molecularfunction_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.organism Structure
| F-Key |
Name |
Type |
Description |
|
|
organismid |
integer |
|
|
|
organismspecies |
text |
|
|
|
organismclassification |
text |
|
|
|
taxonomyxrefdbcode |
integer |
|
|
|
taxonomycode |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.organism Constraints
| Name |
Constraint |
| organism_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| organism_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.project Structure
| F-Key |
Name |
Type |
Description |
|
|
projectid |
integer |
|
|
|
description |
text |
|
|
|
uri |
character varying(4096) |
|
|
|
contactid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.project Constraints
| Name |
Constraint |
| project_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| project_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.reference Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
referenceworkid |
integer |
|
|
|
referencetitle |
text |
|
|
|
referencetypeid |
integer |
|
|
|
referencechecksum |
character(16) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.reference Constraints
| Name |
Constraint |
| reference_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| reference_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencedentry Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
rndisplayedvalue |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencedentry Constraints
| Name |
Constraint |
| referencedentry_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencedentry_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencedgel Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
gelid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencedgel Constraints
| Name |
Constraint |
| referencedgel_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencedgel_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencedobjectparent Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencedobjectparent Constraints
| Name |
Constraint |
| referencedobjectparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencedobjectparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencedproject Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
projectid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencedproject Constraints
| Name |
Constraint |
| referencedproject_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencedproject_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencedsample Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
sampleid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencedsample Constraints
| Name |
Constraint |
| referencedsample_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencedsample_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationbook Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
bookid |
integer |
|
|
|
volume |
smallint |
|
|
|
pagefirst |
integer |
|
|
|
pagelast |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationbook Constraints
| Name |
Constraint |
| referencelocationbook_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationbook_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationjournal Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
journalid |
integer |
|
|
|
volume |
smallint |
|
|
|
subvolume |
smallint |
|
|
|
pagefirst |
integer |
|
|
|
pagelast |
integer |
|
|
|
year |
smallint |
|
|
|
crossreferences |
character varying(128)[] |
|
|
|
unpublished |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationjournal Constraints
| Name |
Constraint |
| referencelocationjournal_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationjournal_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationother Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
text |
text |
|
|
|
personalcomment |
character varying(256) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationother Constraints
| Name |
Constraint |
| referencelocationother_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationother_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationparent Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationparent Constraints
| Name |
Constraint |
| referencelocationparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationpatent Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
patent_publication_number |
character varying(16) |
|
|
|
date |
date |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationpatent Constraints
| Name |
Constraint |
| referencelocationpatent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationpatent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationsubmission Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
month |
smallint |
|
|
|
year |
smallint |
|
|
|
xrefdbcode |
integer |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationsubmission Constraints
| Name |
Constraint |
| referencelocationsubmission_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationsubmission_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationthesis Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
year |
smallint |
|
|
|
institution |
character varying(128) |
|
|
|
country |
character varying(64) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationthesis Constraints
| Name |
Constraint |
| referencelocationthesis_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationthesis_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencelocationunpubobservations Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceid |
integer |
|
|
|
month |
smallint |
|
|
|
year |
smallint |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencelocationunpubobservations Constraints
| Name |
Constraint |
| referencelocationunpubobservations_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencelocationunpubobservations_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencetype Structure
| F-Key |
Name |
Type |
Description |
|
|
referencetypeid |
integer |
|
|
|
referencetype |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencetype Constraints
| Name |
Constraint |
| referencetype_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencetype_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.referencework Structure
| F-Key |
Name |
Type |
Description |
|
|
referenceworkid |
integer |
|
|
|
referenceworkdescription |
character varying(64) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.referencework Constraints
| Name |
Constraint |
| referencework_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| referencework_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.release Structure
| F-Key |
Name |
Type |
Description |
|
|
releasenum |
integer |
|
|
|
subrelease |
smallint |
|
|
|
releasedate |
date |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.release Constraints
| Name |
Constraint |
| release_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| release_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.sample Structure
| F-Key |
Name |
Type |
Description |
|
|
sampleid |
integer |
|
|
|
biosourceid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
samplepreparationid |
integer |
|
|
|
description |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.sample Constraints
| Name |
Constraint |
| sample_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| sample_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.samplepreparation Structure
| F-Key |
Name |
Type |
Description |
|
|
samplepreparationid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
samplepreparationdocument |
text |
|
|
|
samplepreparationprotocol |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.samplepreparation Constraints
| Name |
Constraint |
| samplepreparation_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| samplepreparation_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.secondaryac Structure
| F-Key |
Name |
Type |
Description |
|
|
secondaryac |
character varying(32) |
|
|
|
ac |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.secondaryac Constraints
| Name |
Constraint |
| secondaryac_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| secondaryac_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spot Structure
| F-Key |
Name |
Type |
Description |
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
mw |
integer |
|
|
|
pi |
numeric(4,2) |
|
|
|
xcoordinate |
integer |
|
|
|
ycoordinate |
integer |
|
|
|
odrelative |
real |
|
|
|
volumerelative |
real |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spot Constraints
| Name |
Constraint |
| spot_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spot_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotdataaacid Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
aminoacidlist |
text |
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotdataaacid Constraints
| Name |
Constraint |
| spotdataaacid_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotdataaacid_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotdataother Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
results |
text |
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotdataother Constraints
| Name |
Constraint |
| spotdataother_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotdataother_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotdataparent Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotdataparent Constraints
| Name |
Constraint |
| spotdataparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotdataparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotdatapeptmassf Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
peptidemasses |
double precision[] |
|
|
|
enzyme |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotdatapeptmassf Constraints
| Name |
Constraint |
| spotdatapeptmassf_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotdatapeptmassf_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotdatatandemms Structure
| F-Key |
Name |
Type |
Description |
|
|
dataexpid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
referenceid |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
datadocument |
text |
|
|
|
experimentdescription |
text |
|
|
|
experimentdate |
date |
|
|
|
appreciation |
smallint |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
parentmass |
double precision |
|
|
|
parentcharge |
smallint |
|
|
|
ionmasses |
double precision[] |
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotdatatandemms Constraints
| Name |
Constraint |
| spotdatatandemms_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotdatatandemms_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotentry Structure
| F-Key |
Name |
Type |
Description |
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
fragment |
boolean |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotentry Constraints
| Name |
Constraint |
| spotentry_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotentry_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotentrygeneraltopic Structure
| F-Key |
Name |
Type |
Description |
|
|
topicdataid |
integer |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotentrygeneraltopic Constraints
| Name |
Constraint |
| spotentrygeneraltopic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotentrygeneraltopic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotentrymappingtopic Structure
| F-Key |
Name |
Type |
Description |
|
|
topicdataid |
integer |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
mappingtechnique |
character varying(8)[] |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotentrymappingtopic Constraints
| Name |
Constraint |
| spotentrymappingtopic_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotentrymappingtopic_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotentrytopicparent Structure
| F-Key |
Name |
Type |
Description |
|
|
topicdataid |
integer |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
|
|
|
usermodifiername |
character varying(128) |
|
log.spotentrytopicparent Constraints
| Name |
Constraint |
| spotentrytopicparent_modificationdate_check |
CHECK ((modificationdate IS NOT NULL)) |
| spotentrytopicparent_updatedordeleted_check |
CHECK (((updatedordeleted = 'U'::bpchar) OR (updatedordeleted = 'D'::bpchar))) |
Index -
Schema log
log.spotidentificationaacid Structure
| F-Key |
Name |
Type |
Description |
|
|
identificationid |
integer |
|
|
|
humanidentifier |
character varying(256) |
|
|
|
hassubset |
boolean |
|
|
|
dataexpid |
integer |
|
|
|
spotid |
character varying(16) |
|
|
|
gelid |
integer |
|
|
|
ac |
character varying(32) |
|
|
|
isoform |
text |
|
|
|
version |
integer |
|
|
|
contactid |
integer |
|
|
|
uri |
character varying(4096) |
|
|
|
identificationdocument |
text |
|
|
|
identificationdescription |
text |
|
|
|
allexperimentdata |
boolean |
|
|
|
appreciation |
numeric(2,1) |
|
|
|
datadisplayer |
text |
|
|
|
showflag |
boolean |
|
|
|
showflagswitch |
boolean |
|
|
|
aminoacidlist |
text |
|
|
|
relateddata |
text |
|
|
|
userstamp |
character varying(128) |
|
|
|
modificationdate |
timestamp without time zone |
DEFAULT now()
|
|
|
updatedordeleted |
character(1) |
